PDB Short entry for 2VO9 HEADER HYDROLASE 09-FEB-08 2VO9 TITLE CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA TITLE 2 MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500 COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ALANYL-D-GLUTAMATE PEPTIDASE; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 1-167; COMPND 5 SYNONYM: EAD500; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE A500; SOURCE 3 ORGANISM_TAXID: 40522; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM83; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PEACE500.7 KEYWDS CELL WALL BIOGENESIS/DEGRADATION, SECRETED, CELL WALL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.P.KORNDOERFER,A.KANITZ,A.SKERRA REVDAT 6 27-FEB-19 2VO9 1 REMARK REVDAT 5 30-JAN-19 2VO9 1 REMARK REVDAT 4 05-JUL-17 2VO9 1 REMARK REVDAT 3 10-AUG-11 2VO9 1 KEYWDS JRNL REMARK FORMUL REVDAT 3 2 1 MASTER VERSN REVDAT 2 24-FEB-09 2VO9 1 VERSN REVDAT 1 19-FEB-08 2VO9 0 SPRSDE 19-FEB-08 2VO9 1XP2 JRNL AUTH I.P.KORNDORFER,A.KANITZ,J.DANZER,M.ZIMMER,M.J.LOESSNER, JRNL AUTH 2 A.SKERRA JRNL TITL STRUCTURAL ANALYSIS OF THE L-ALANOYL-D-GLUTAMATE JRNL TITL 2 ENDOPEPTIDASE DOMAIN OF LISTERIA BACTERIOPHAGE ENDOLYSIN JRNL TITL 3 PLY500 REVEALS A NEW MEMBER OF THE LAS PEPTIDASE FAMILY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 644 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18560152 JRNL DOI 10.1107/S0907444908007890 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 44421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2392 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3340 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3459 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 369 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 0.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.216 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3555 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4794 ; 1.628 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 6.587 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;28.191 ;24.490 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 627 ;14.556 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.487 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 504 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2628 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1641 ; 0.210 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2399 ; 0.310 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 487 ; 0.194 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 73 ; 0.207 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 58 ; 0.195 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2246 ; 1.672 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3486 ; 2.211 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1553 ; 2.058 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1308 ; 2.730 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 503 6 REMARK 3 1 B 0 B 503 6 REMARK 3 1 C 0 C 503 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 1164 ; 0.35 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 1164 ; 0.34 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 C (A): 1164 ; 0.39 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 1164 ; 1.98 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 1164 ; 1.81 ; 10.00 REMARK 3 LOOSE THERMAL 1 C (A**2): 1164 ; 2.87 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.66 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL2MAP, SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 2.4% PEG 400, 1.7M REMARK 280 (NH4)2SO4, PH 7.5, VAPOR DIFFUSION, HANGING DROP, 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.28900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.28900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.89350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.59000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.89350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.59000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.28900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.89350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.59000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 91.28900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.89350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.59000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2027 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A -11 REMARK 465 SER A -10 REMARK 465 TRP A -9 REMARK 465 SER A -8 REMARK 465 HIS A -7 REMARK 465 PRO A -6 REMARK 465 GLN A -5 REMARK 465 PHE A -4 REMARK 465 GLU A -3 REMARK 465 LYS A -2 REMARK 465 GLY A -1 REMARK 465 THR A 149 REMARK 465 GLN A 150 REMARK 465 ASN A 151 REMARK 465 THR A 152 REMARK 465 ASN A 153 REMARK 465 THR A 154 REMARK 465 ASN A 155 REMARK 465 SER A 156 REMARK 465 ASN A 157 REMARK 465 ARG A 158 REMARK 465 TYR A 159 REMARK 465 GLU A 160 REMARK 465 GLY A 161 REMARK 465 LYS A 162 REMARK 465 VAL A 163 REMARK 465 ILE A 164 REMARK 465 ASP A 165 REMARK 465 SER A 166 REMARK 465 ALA A 167 REMARK 465 ALA B -11 REMARK 465 SER B -10 REMARK 465 TRP B -9 REMARK 465 SER B -8 REMARK 465 HIS B -7 REMARK 465 PRO B -6 REMARK 465 GLN B -5 REMARK 465 PHE B -4 REMARK 465 GLU B -3 REMARK 465 LYS B -2 REMARK 465 GLY B -1 REMARK 465 THR B 149 REMARK 465 GLN B 150 REMARK 465 ASN B 151 REMARK 465 THR B 152 REMARK 465 ASN B 153 REMARK 465 THR B 154 REMARK 465 ASN B 155 REMARK 465 SER B 156 REMARK 465 ASN B 157 REMARK 465 ARG B 158 REMARK 465 TYR B 159 REMARK 465 GLU B 160 REMARK 465 GLY B 161 REMARK 465 LYS B 162 REMARK 465 VAL B 163 REMARK 465 ILE B 164 REMARK 465 ASP B 165 REMARK 465 SER B 166 REMARK 465 ALA B 167 REMARK 465 ALA C -11 REMARK 465 SER C -10 REMARK 465 TRP C -9 REMARK 465 SER C -8 REMARK 465 HIS C -7 REMARK 465 PRO C -6 REMARK 465 GLN C -5 REMARK 465 PHE C -4 REMARK 465 GLU C -3 REMARK 465 LYS C -2 REMARK 465 GLY C -1 REMARK 465 THR C 149 REMARK 465 GLN C 150 REMARK 465 ASN C 151 REMARK 465 THR C 152 REMARK 465 ASN C 153 REMARK 465 THR C 154 REMARK 465 ASN C 155 REMARK 465 SER C 156 REMARK 465 ASN C 157 REMARK 465 ARG C 158 REMARK 465 TYR C 159 REMARK 465 GLU C 160 REMARK 465 GLY C 161 REMARK 465 LYS C 162 REMARK 465 VAL C 163 REMARK 465 ILE C 164 REMARK 465 ASP C 165 REMARK 465 SER C 166 REMARK 465 ALA C 167 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 2032 O HOH B 2069 1.67 REMARK 500 O HOH B 2051 O HOH B 2109 1.80 REMARK 500 O HOH A 2017 O HOH A 2053 2.15 REMARK 500 OD1 ASN C 17 NH2 ARG C 30 2.17 REMARK 500 O HOH B 2033 O HOH B 2072 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 30 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG B 30 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG B 106 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 106 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG C 30 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG C 30 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG B 63 -68.97 -122.57 REMARK 500 ARG C 63 -70.54 -115.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 147 ALA A 148 149.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2045 DISTANCE = 5.86 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 80 NE2 REMARK 620 2 HIS A 133 ND1 107.0 REMARK 620 3 ASP A 87 OD2 104.3 114.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2146 O REMARK 620 2 HIS B 80 NE2 121.6 REMARK 620 3 ASP B 87 OD2 107.4 108.0 REMARK 620 4 HIS B 133 ND1 102.9 104.1 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 133 ND1 REMARK 620 2 ASP C 87 OD2 114.1 REMARK 620 3 HIS C 80 NE2 105.6 102.5 REMARK 620 N 1 2 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 503 DBREF 2VO9 A -11 0 PDB 2VO9 2VO9 -11 0 DBREF 2VO9 A 1 167 UNP Q37979 AEPE_BPA50 1 167 DBREF 2VO9 B -11 0 PDB 2VO9 2VO9 -11 0 DBREF 2VO9 B 1 167 UNP Q37979 AEPE_BPA50 1 167 DBREF 2VO9 C -11 0 PDB 2VO9 2VO9 -11 0 DBREF 2VO9 C 1 167 UNP Q37979 AEPE_BPA50 1 167 SEQRES 1 A 179 ALA SER TRP SER HIS PRO GLN PHE GLU LYS GLY ALA MET SEQRES 2 A 179 ALA LEU THR GLU ALA TRP LEU ILE GLU LYS ALA ASN ARG SEQRES 3 A 179 LYS LEU ASN ALA GLY GLY MET TYR LYS ILE THR SER ASP SEQRES 4 A 179 LYS THR ARG ASN VAL ILE LYS LYS MET ALA LYS GLU GLY SEQRES 5 A 179 ILE TYR LEU CYS VAL ALA GLN GLY TYR ARG SER THR ALA SEQRES 6 A 179 GLU GLN ASN ALA LEU TYR ALA GLN GLY ARG THR LYS PRO SEQRES 7 A 179 GLY ALA ILE VAL THR ASN ALA LYS GLY GLY GLN SER ASN SEQRES 8 A 179 HIS ASN TYR GLY VAL ALA VAL ASP LEU CYS LEU TYR THR SEQRES 9 A 179 ASN ASP GLY LYS ASP VAL ILE TRP GLU SER THR THR SER SEQRES 10 A 179 ARG TRP LYS LYS VAL VAL ALA ALA MET LYS ALA GLU GLY SEQRES 11 A 179 PHE LYS TRP GLY GLY ASP TRP LYS SER PHE LYS ASP TYR SEQRES 12 A 179 PRO HIS PHE GLU LEU CYS ASP ALA VAL SER GLY GLU LYS SEQRES 13 A 179 ILE PRO ALA ALA THR GLN ASN THR ASN THR ASN SER ASN SEQRES 14 A 179 ARG TYR GLU GLY LYS VAL ILE ASP SER ALA SEQRES 1 B 179 ALA SER TRP SER HIS PRO GLN PHE GLU LYS GLY ALA MET SEQRES 2 B 179 ALA LEU THR GLU ALA TRP LEU ILE GLU LYS ALA ASN ARG SEQRES 3 B 179 LYS LEU ASN ALA GLY GLY MET TYR LYS ILE THR SER ASP SEQRES 4 B 179 LYS THR ARG ASN VAL ILE LYS LYS MET ALA LYS GLU GLY SEQRES 5 B 179 ILE TYR LEU CYS VAL ALA GLN GLY TYR ARG SER THR ALA SEQRES 6 B 179 GLU GLN ASN ALA LEU TYR ALA GLN GLY ARG THR LYS PRO SEQRES 7 B 179 GLY ALA ILE VAL THR ASN ALA LYS GLY GLY GLN SER ASN SEQRES 8 B 179 HIS ASN TYR GLY VAL ALA VAL ASP LEU CYS LEU TYR THR SEQRES 9 B 179 ASN ASP GLY LYS ASP VAL ILE TRP GLU SER THR THR SER SEQRES 10 B 179 ARG TRP LYS LYS VAL VAL ALA ALA MET LYS ALA GLU GLY SEQRES 11 B 179 PHE LYS TRP GLY GLY ASP TRP LYS SER PHE LYS ASP TYR SEQRES 12 B 179 PRO HIS PHE GLU LEU CYS ASP ALA VAL SER GLY GLU LYS SEQRES 13 B 179 ILE PRO ALA ALA THR GLN ASN THR ASN THR ASN SER ASN SEQRES 14 B 179 ARG TYR GLU GLY LYS VAL ILE ASP SER ALA SEQRES 1 C 179 ALA SER TRP SER HIS PRO GLN PHE GLU LYS GLY ALA MET SEQRES 2 C 179 ALA LEU THR GLU ALA TRP LEU ILE GLU LYS ALA ASN ARG SEQRES 3 C 179 LYS LEU ASN ALA GLY GLY MET TYR LYS ILE THR SER ASP SEQRES 4 C 179 LYS THR ARG ASN VAL ILE LYS LYS MET ALA LYS GLU GLY SEQRES 5 C 179 ILE TYR LEU CYS VAL ALA GLN GLY TYR ARG SER THR ALA SEQRES 6 C 179 GLU GLN ASN ALA LEU TYR ALA GLN GLY ARG THR LYS PRO SEQRES 7 C 179 GLY ALA ILE VAL THR ASN ALA LYS GLY GLY GLN SER ASN SEQRES 8 C 179 HIS ASN TYR GLY VAL ALA VAL ASP LEU CYS LEU TYR THR SEQRES 9 C 179 ASN ASP GLY LYS ASP VAL ILE TRP GLU SER THR THR SER SEQRES 10 C 179 ARG TRP LYS LYS VAL VAL ALA ALA MET LYS ALA GLU GLY SEQRES 11 C 179 PHE LYS TRP GLY GLY ASP TRP LYS SER PHE LYS ASP TYR SEQRES 12 C 179 PRO HIS PHE GLU LEU CYS ASP ALA VAL SER GLY GLU LYS SEQRES 13 C 179 ILE PRO ALA ALA THR GLN ASN THR ASN THR ASN SER ASN SEQRES 14 C 179 ARG TYR GLU GLY LYS VAL ILE ASP SER ALA HET ZN A 501 1 HET SO4 A 502 5 HET SO4 A 503 5 HET ZN B 501 1 HET SO4 B 502 5 HET SO4 B 503 5 HET ZN C 501 1 HET SO4 C 502 5 HET SO4 C 503 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 4 ZN 3(ZN 2+) FORMUL 5 SO4 6(O4 S 2-) FORMUL 13 HOH *369(H2 O) HELIX 1 1 THR A 4 ASN A 17 1 14 HELIX 2 2 TYR A 22 LYS A 38 1 17 HELIX 3 3 SER A 51 GLN A 61 1 11 HELIX 4 4 SER A 78 GLY A 83 5 6 HELIX 5 5 THR A 104 GLU A 117 1 14 HELIX 6 6 GLY A 123 TRP A 125 5 3 HELIX 7 7 ASP A 138 GLY A 142 5 5 HELIX 8 8 THR B 4 ASN B 17 1 14 HELIX 9 9 TYR B 22 LYS B 38 1 17 HELIX 10 10 SER B 51 GLN B 61 1 11 HELIX 11 11 SER B 78 GLY B 83 5 6 HELIX 12 12 THR B 104 GLU B 117 1 14 HELIX 13 13 GLY B 123 TRP B 125 5 3 HELIX 14 14 THR C 4 ASN C 17 1 14 HELIX 15 15 TYR C 22 LYS C 38 1 17 HELIX 16 16 SER C 51 GLN C 61 1 11 HELIX 17 17 SER C 78 GLY C 83 5 6 HELIX 18 18 THR C 104 GLU C 117 1 14 HELIX 19 19 GLY C 123 TRP C 125 5 3 SHEET 1 AA 4 LEU A 43 GLN A 47 0 SHEET 2 AA 4 ALA A 85 TYR A 91 -1 O ASP A 87 N ALA A 46 SHEET 3 AA 4 HIS A 133 GLU A 135 -1 O PHE A 134 N VAL A 86 SHEET 4 AA 4 LYS A 120 TRP A 121 -1 O LYS A 120 N GLU A 135 SHEET 1 AB 3 LEU A 43 GLN A 47 0 SHEET 2 AB 3 ALA A 85 TYR A 91 -1 O ASP A 87 N ALA A 46 SHEET 3 AB 3 VAL A 98 ILE A 99 -1 O ILE A 99 N LEU A 90 SHEET 1 BA 4 LEU B 43 GLN B 47 0 SHEET 2 BA 4 ALA B 85 TYR B 91 -1 O ASP B 87 N ALA B 46 SHEET 3 BA 4 HIS B 133 GLU B 135 -1 O PHE B 134 N VAL B 86 SHEET 4 BA 4 LYS B 120 TRP B 121 -1 O LYS B 120 N GLU B 135 SHEET 1 BB 3 LEU B 43 GLN B 47 0 SHEET 2 BB 3 ALA B 85 TYR B 91 -1 O ASP B 87 N ALA B 46 SHEET 3 BB 3 VAL B 98 ILE B 99 -1 O ILE B 99 N LEU B 90 SHEET 1 CA 4 LEU C 43 GLN C 47 0 SHEET 2 CA 4 ALA C 85 TYR C 91 -1 O ASP C 87 N ALA C 46 SHEET 3 CA 4 HIS C 133 GLU C 135 -1 O PHE C 134 N VAL C 86 SHEET 4 CA 4 LYS C 120 TRP C 121 -1 O LYS C 120 N GLU C 135 SHEET 1 CB 3 LEU C 43 GLN C 47 0 SHEET 2 CB 3 ALA C 85 TYR C 91 -1 O ASP C 87 N ALA C 46 SHEET 3 CB 3 VAL C 98 ILE C 99 -1 O ILE C 99 N LEU C 90 LINK ZN ZN A 501 NE2 HIS A 80 1555 1555 2.03 LINK ZN ZN A 501 ND1 HIS A 133 1555 1555 2.04 LINK ZN ZN A 501 OD2 ASP A 87 1555 1555 1.98 LINK ZN ZN B 501 O HOH B2146 1555 1555 1.94 LINK ZN ZN B 501 NE2 HIS B 80 1555 1555 2.00 LINK ZN ZN B 501 OD2 ASP B 87 1555 1555 2.01 LINK ZN ZN B 501 ND1 HIS B 133 1555 1555 2.04 LINK ZN ZN C 501 ND1 HIS C 133 1555 1555 2.07 LINK ZN ZN C 501 OD2 ASP C 87 1555 1555 2.06 LINK ZN ZN C 501 NE2 HIS C 80 1555 1555 2.02 SITE 1 AC1 3 HIS A 80 ASP A 87 HIS A 133 SITE 1 AC2 8 ARG A 50 GLN A 55 THR A 71 SER A 78 SITE 2 AC2 8 HIS A 80 HOH A2080 HOH A2131 HOH A2132 SITE 1 AC3 8 TRP A 7 LYS A 11 LYS A 96 HOH A2085 SITE 2 AC3 8 HOH A2133 LYS B 126 PHE B 128 LYS B 129 SITE 1 AC4 4 HIS B 80 ASP B 87 HIS B 133 HOH B2146 SITE 1 AC5 8 ARG B 50 GLN B 55 THR B 71 SER B 78 SITE 2 AC5 8 HIS B 80 HOH B2092 HOH B2147 HOH B2148 SITE 1 AC6 8 LYS A 126 PHE A 128 LYS A 129 TRP B 7 SITE 2 AC6 8 LYS B 11 LYS B 96 HOH B2097 HOH B2149 SITE 1 AC7 3 HIS C 80 ASP C 87 HIS C 133 SITE 1 AC8 6 ARG C 50 GLN C 55 THR C 71 SER C 78 SITE 2 AC8 6 HIS C 80 HOH C2048 SITE 1 AC9 9 TRP C 7 LYS C 11 LYS C 96 LYS C 126 SITE 2 AC9 9 SER C 127 PHE C 128 LYS C 129 HOH C2051 SITE 3 AC9 9 HOH C2087 CRYST1 59.787 95.180 182.578 90.00 90.00 90.00 C 2 2 21 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005477 0.00000 MTRIX1 1 -0.431207 -0.902237 0.005387 97.37700 1 MTRIX2 1 -0.902247 0.431218 0.001199 28.18880 1 MTRIX3 1 -0.003405 -0.004344 -0.999985 61.17760 1 MTRIX1 2 0.499480 0.866322 0.002399 17.67400 1 MTRIX2 2 -0.863428 0.497582 0.083086 19.54960 1 MTRIX3 2 0.070786 -0.043571 0.996539 30.46440 1