PDB Short entry for 2NO5 HEADER HYDROLASE 24-OCT-06 2NO5 TITLE CRYSTAL STRUCTURE ANALYSIS OF A DEHALOGENASE WITH INTERMEDIATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: (S)-2-HALOACID DEHALOGENASE IVA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEHALOGENASE, 2-HALOALKANOIC ACID DEHALOGENASE IVA, L-2- COMPND 5 HALOACID DEHALOGENASE IVA, HALOCARBOXYLIC ACID HALIDOHYDROLASE IVA; COMPND 6 EC: 3.8.1.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA CEPACIA; SOURCE 3 ORGANISM_TAXID: 292; SOURCE 4 STRAIN: MBA4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHKU201 KEYWDS HALOACID DEHALOGENASE, DEHALOGENASE, HAD SUPERFAMILY, INTERMEDIATE KEYWDS 2 STRUCTURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.W.SCHMIDBERGER,M.C.J.WILCE REVDAT 5 15-NOV-23 2NO5 1 REMARK REVDAT 4 25-OCT-23 2NO5 1 SEQADV LINK REVDAT 3 13-JUL-11 2NO5 1 VERSN REVDAT 2 24-FEB-09 2NO5 1 VERSN REVDAT 1 25-SEP-07 2NO5 0 JRNL AUTH J.W.SCHMIDBERGER,J.A.WILCE,J.S.H.TSANG,M.C.J.WILCE JRNL TITL CRYSTAL STRUCTURES OF THE SUBSTRATE FREE-ENZYME, AND JRNL TITL 2 REACTION INTERMEDIATE OF THE HAD SUPERFAMILY MEMBER, JRNL TITL 3 HALOACID DEHALOGENASE DEHIVA FROM BURKHOLDERIA CEPACIA MBA4 JRNL REF J.MOL.BIOL. V. 368 706 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17368477 JRNL DOI 10.1016/J.JMB.2007.02.015 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25671 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1315 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1837 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3592 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.324 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.189 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.856 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3791 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5148 ; 1.845 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 7.057 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;40.664 ;24.153 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 639 ;20.261 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.918 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2864 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1855 ; 0.243 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2553 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 191 ; 0.161 ; 0.200 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): 44 ; 0.221 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.259 ; 0.200 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): 2303 ; 1.859 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3622 ; 3.011 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1683 ; 1.817 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1525 ; 2.741 ; 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 : NULL 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 : 1.20 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 2NO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.8 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26322 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.490 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.11 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2NO4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.65M AMMONIUM SULPHATE, REMARK 280 PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.93133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.86267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.86267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.93133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE STRUCTURE IS A FUNCTIONAL HOMODIMER IN THE ASU. ASP11 REMARK 300 ON EACH CHAIN (A AND B) IS COVALENTLY BOUND TO A REACTION REMARK 300 INTERMEDIATE, OF THE SUBSTRATE L-2-MONOCHLOROPRAPANATE. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -228.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.93133 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 B1022 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 MET A -8 REMARK 465 ASP A -7 REMARK 465 TYR A -6 REMARK 465 LYS A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 LYS A 0 REMARK 465 ASN A 226 REMARK 465 VAL A 227 REMARK 465 THR A 228 REMARK 465 LYS A 229 REMARK 465 ALA A 230 REMARK 465 ALA A 231 REMARK 465 MET B -8 REMARK 465 ASP B -7 REMARK 465 TYR B -6 REMARK 465 LYS B -5 REMARK 465 ASP B -4 REMARK 465 ASP B -3 REMARK 465 ASP B -2 REMARK 465 ASP B -1 REMARK 465 LYS B 0 REMARK 465 VAL B 227 REMARK 465 THR B 228 REMARK 465 LYS B 229 REMARK 465 ALA B 230 REMARK 465 ALA B 231 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 33 OG SER A 33 6555 2.12 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 ASP A 146 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 181 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 87 NE - CZ - NH1 ANGL. DEV. = 3.6 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 VAL A 2 -47.51 -132.46 REMARK 500 ASP A 3 46.64 -144.30 REMARK 500 ALA A 12 -75.34 -90.84 REMARK 500 ALA B 12 -67.64 -91.64 REMARK 500 TYR B 13 96.34 -66.40 REMARK 500 ARG B 25 -16.42 -45.80 REMARK 500 PRO B 153 36.23 -91.20 REMARK 500 ALA B 207 73.26 -118.38 REMARK 500 SER B 215 142.34 -171.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NO4 RELATED DB: PDB REMARK 900 ENZYME WITHOUT INTERMEDIATE COMPLEX DBREF 2NO5 A 2 231 UNP Q51645 HAD4_BURCE 1 230 DBREF 2NO5 B 2 231 UNP Q51645 HAD4_BURCE 1 230 SEQADV 2NO5 MET A -8 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP A -7 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 TYR A -6 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LYS A -5 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP A -4 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP A -3 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP A -2 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP A -1 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LYS A 0 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LEU A 1 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASL A 11 UNP Q51645 ASP 10 MODIFIED RESIDUE SEQADV 2NO5 MET B -8 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP B -7 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 TYR B -6 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LYS B -5 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP B -4 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP B -3 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP B -2 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASP B -1 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LYS B 0 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 LEU B 1 UNP Q51645 EXPRESSION TAG SEQADV 2NO5 ASL B 11 UNP Q51645 ASP 10 MODIFIED RESIDUE SEQRES 1 A 240 MET ASP TYR LYS ASP ASP ASP ASP LYS LEU VAL ASP SER SEQRES 2 A 240 LEU ARG ALA CYS VAL PHE ASL ALA TYR GLY THR LEU LEU SEQRES 3 A 240 ASP VAL HIS SER ALA VAL MET ARG ASN ALA ASP GLU VAL SEQRES 4 A 240 GLY ALA SER ALA GLU ALA LEU SER MET LEU TRP ARG GLN SEQRES 5 A 240 ARG GLN LEU GLU TYR SER TRP THR ARG THR LEU MET HIS SEQRES 6 A 240 GLN TYR ALA ASP PHE TRP GLN LEU THR ASP GLU ALA LEU SEQRES 7 A 240 THR PHE ALA LEU ARG THR TYR HIS LEU GLU ASP ARG LYS SEQRES 8 A 240 GLY LEU LYS ASP ARG LEU MET SER ALA TYR LYS GLU LEU SEQRES 9 A 240 SER ALA TYR PRO ASP ALA ALA GLU THR LEU GLU LYS LEU SEQRES 10 A 240 LYS SER ALA GLY TYR ILE VAL ALA ILE LEU SER ASN GLY SEQRES 11 A 240 ASN ASP GLU MET LEU GLN ALA ALA LEU LYS ALA SER LYS SEQRES 12 A 240 LEU ASP ARG VAL LEU ASP SER CYS LEU SER ALA ASP ASP SEQRES 13 A 240 LEU LYS ILE TYR LYS PRO ASP PRO ARG ILE TYR GLN PHE SEQRES 14 A 240 ALA CYS ASP ARG LEU GLY VAL ASN PRO ASN GLU VAL CYS SEQRES 15 A 240 PHE VAL SER SER ASN ALA TRP ASP LEU GLY GLY ALA GLY SEQRES 16 A 240 LYS PHE GLY PHE ASN THR VAL ARG ILE ASN ARG GLN GLY SEQRES 17 A 240 ASN PRO PRO GLU TYR GLU PHE ALA PRO LEU LYS HIS GLN SEQRES 18 A 240 VAL ASN SER LEU SER GLU LEU TRP PRO LEU LEU ALA LYS SEQRES 19 A 240 ASN VAL THR LYS ALA ALA SEQRES 1 B 240 MET ASP TYR LYS ASP ASP ASP ASP LYS LEU VAL ASP SER SEQRES 2 B 240 LEU ARG ALA CYS VAL PHE ASL ALA TYR GLY THR LEU LEU SEQRES 3 B 240 ASP VAL HIS SER ALA VAL MET ARG ASN ALA ASP GLU VAL SEQRES 4 B 240 GLY ALA SER ALA GLU ALA LEU SER MET LEU TRP ARG GLN SEQRES 5 B 240 ARG GLN LEU GLU TYR SER TRP THR ARG THR LEU MET HIS SEQRES 6 B 240 GLN TYR ALA ASP PHE TRP GLN LEU THR ASP GLU ALA LEU SEQRES 7 B 240 THR PHE ALA LEU ARG THR TYR HIS LEU GLU ASP ARG LYS SEQRES 8 B 240 GLY LEU LYS ASP ARG LEU MET SER ALA TYR LYS GLU LEU SEQRES 9 B 240 SER ALA TYR PRO ASP ALA ALA GLU THR LEU GLU LYS LEU SEQRES 10 B 240 LYS SER ALA GLY TYR ILE VAL ALA ILE LEU SER ASN GLY SEQRES 11 B 240 ASN ASP GLU MET LEU GLN ALA ALA LEU LYS ALA SER LYS SEQRES 12 B 240 LEU ASP ARG VAL LEU ASP SER CYS LEU SER ALA ASP ASP SEQRES 13 B 240 LEU LYS ILE TYR LYS PRO ASP PRO ARG ILE TYR GLN PHE SEQRES 14 B 240 ALA CYS ASP ARG LEU GLY VAL ASN PRO ASN GLU VAL CYS SEQRES 15 B 240 PHE VAL SER SER ASN ALA TRP ASP LEU GLY GLY ALA GLY SEQRES 16 B 240 LYS PHE GLY PHE ASN THR VAL ARG ILE ASN ARG GLN GLY SEQRES 17 B 240 ASN PRO PRO GLU TYR GLU PHE ALA PRO LEU LYS HIS GLN SEQRES 18 B 240 VAL ASN SER LEU SER GLU LEU TRP PRO LEU LEU ALA LYS SEQRES 19 B 240 ASN VAL THR LYS ALA ALA MODRES 2NO5 ASL A 11 ASP ASPARTIC ACID-4-CARBOXYETHYL ESTER MODRES 2NO5 ASL B 11 ASP ASPARTIC ACID-4-CARBOXYETHYL ESTER HET ASL A 11 13 HET ASL B 11 13 HET CL A 232 1 HET SO4 A1001 5 HET SO4 A1002 5 HET SO4 A1006 5 HET SO4 A1007 5 HET SO4 A1008 5 HET SO4 A1011 5 HET CNR A1015 6 HET SO4 B1003 5 HET SO4 B1004 5 HET SO4 B1005 5 HET SO4 B1009 5 HET SO4 B1010 5 HET SO4 B1012 5 HET SO4 B1013 5 HET CNR B1014 6 HET CNR B1016 6 HETNAM ASL ASPARTIC ACID-4-CARBOXYETHYL ESTER HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM CNR (2S)-2-CHLOROPROPANOIC ACID HETSYN CNR 2-MONOCHLOROPRAPANATE FORMUL 1 ASL 2(C7 H11 N O6) FORMUL 3 CL CL 1- FORMUL 4 SO4 13(O4 S 2-) FORMUL 10 CNR 3(C3 H5 CL O2) FORMUL 20 HOH *89(H2 O) HELIX 1 1 VAL A 19 ARG A 25 1 7 HELIX 2 2 ASN A 26 GLY A 31 1 6 HELIX 3 3 SER A 33 MET A 55 1 23 HELIX 4 4 ASP A 60 TYR A 76 1 17 HELIX 5 5 ASP A 80 GLU A 94 1 15 HELIX 6 6 ASP A 100 ALA A 111 1 12 HELIX 7 7 ASN A 122 SER A 133 1 12 HELIX 8 8 LEU A 135 LEU A 139 5 5 HELIX 9 9 ASP A 154 GLY A 166 1 13 HELIX 10 10 ASN A 168 ASN A 170 5 3 HELIX 11 11 ASN A 178 GLY A 189 1 12 HELIX 12 12 GLU A 218 ALA A 224 1 7 HELIX 13 13 VAL B 19 ARG B 25 1 7 HELIX 14 14 ASN B 26 GLY B 31 1 6 HELIX 15 15 SER B 33 MET B 55 1 23 HELIX 16 16 ASP B 60 TYR B 76 1 17 HELIX 17 17 ASP B 80 GLU B 94 1 15 HELIX 18 18 ASP B 100 SER B 110 1 11 HELIX 19 19 ASN B 122 SER B 133 1 12 HELIX 20 20 LEU B 135 LEU B 139 5 5 HELIX 21 21 ALA B 145 LYS B 149 1 5 HELIX 22 22 ASP B 154 GLY B 166 1 13 HELIX 23 23 ASN B 168 ASN B 170 5 3 HELIX 24 24 ASN B 178 GLY B 189 1 12 HELIX 25 25 SER B 215 SER B 217 5 3 HELIX 26 26 GLU B 218 ALA B 224 1 7 SHEET 1 A 6 SER A 141 SER A 144 0 SHEET 2 A 6 ILE A 114 SER A 119 1 N ILE A 117 O SER A 141 SHEET 3 A 6 ALA A 7 PHE A 10 1 N PHE A 10 O ALA A 116 SHEET 4 A 6 VAL A 172 SER A 176 1 O CYS A 173 N ALA A 7 SHEET 5 A 6 ASN A 191 ILE A 195 1 O ASN A 191 N PHE A 174 SHEET 6 A 6 HIS A 211 VAL A 213 1 O VAL A 213 N ARG A 194 SHEET 1 B 6 SER B 141 SER B 144 0 SHEET 2 B 6 ILE B 114 SER B 119 1 N ILE B 117 O LEU B 143 SHEET 3 B 6 ALA B 7 PHE B 10 1 N PHE B 10 O ALA B 116 SHEET 4 B 6 VAL B 172 SER B 176 1 O CYS B 173 N ALA B 7 SHEET 5 B 6 ASN B 191 ILE B 195 1 O ASN B 191 N PHE B 174 SHEET 6 B 6 HIS B 211 VAL B 213 1 O VAL B 213 N ARG B 194 LINK C PHE A 10 N ASL A 11 1555 1555 1.33 LINK C ASL A 11 N ALA A 12 1555 1555 1.34 LINK C PHE B 10 N ASL B 11 1555 1555 1.32 LINK C ASL B 11 N ALA B 12 1555 1555 1.32 CISPEP 1 LYS A 152 PRO A 153 0 0.35 CISPEP 2 LYS B 152 PRO B 153 0 -0.28 CRYST1 103.743 103.743 134.794 90.00 90.00 120.00 P 31 2 1 12 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 0.009639 0.005565 0.000000 0.00000 SCALE2 0.000000 0.011130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007419 0.00000