PDB Short entry for 3DA4 HEADER ANTIBIOTIC 28-MAY-08 3DA4 TITLE CRYSTAL STRUCTURE OF COLICIN M, A NOVEL PHOSPHATASE SPECIFICALLY TITLE 2 IMPORTED BY ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-M; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COLICIN M, PHOSPHATASE, ANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, KEYWDS 2 PLASMID, TONB BOX EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH,R.ALBRECHT,C.ROMER,V.BRAUN REVDAT 6 01-NOV-23 3DA4 1 REMARK SEQADV REVDAT 5 25-OCT-17 3DA4 1 REMARK REVDAT 4 24-FEB-09 3DA4 1 VERSN REVDAT 3 07-OCT-08 3DA4 1 JRNL AUTHOR REVDAT 2 05-AUG-08 3DA4 1 REMARK REVDAT 1 29-JUL-08 3DA4 0 JRNL AUTH K.ZETH,C.ROMER,S.I.PATZER,V.BRAUN JRNL TITL CRYSTAL STRUCTURE OF COLICIN M, A NOVEL PHOSPHATASE JRNL TITL 2 SPECIFICALLY IMPORTED BY ESCHERICHIA COLI JRNL REF J.BIOL.CHEM. V. 283 25324 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18640984 JRNL DOI 10.1074/JBC.M802591200 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 62343 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4692 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4274 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 321 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4135 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 641 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.44000 REMARK 3 B33 (A**2) : 0.65000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.659 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4258 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5789 ; 1.771 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 540 ; 6.577 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;34.078 ;24.335 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 677 ;14.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;17.405 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 648 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3236 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4119 ; 0.255 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3197 ; 0.341 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 873 ; 0.203 ; 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): 217 ; 0.251 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 52 ; 0.184 ; 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): 2723 ; 0.711 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4334 ; 1.172 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1698 ; 1.967 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1454 ; 2.958 ; 4.500 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 4 A 130 5 REMARK 3 1 B 4 B 130 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 508 ; 0.09 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 464 ; 0.33 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 508 ; 0.61 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 464 ; 1.00 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 180 A 260 5 REMARK 3 1 B 180 B 260 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 324 ; 0.13 ; 0.50 REMARK 3 LOOSE POSITIONAL 2 A (A): 303 ; 0.20 ; 5.00 REMARK 3 MEDIUM THERMAL 2 A (A**2): 324 ; 0.60 ; 2.00 REMARK 3 LOOSE THERMAL 2 A (A**2): 303 ; 1.36 ; 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 3DA4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67044 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.45200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DA3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M N-(2-ACETAMIDO) IMINODIACETATE, REMARK 280 12% PEG 6000, 0.2M MGCL2, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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 112.47000 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 112.47000 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 25.24500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.24500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 112.47000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.24500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.37500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 112.47000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.24500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.37500 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 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 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 1 REMARK 465 ALA A 272 REMARK 465 ALA A 273 REMARK 465 HIS A 274 REMARK 465 HIS A 275 REMARK 465 HIS A 276 REMARK 465 HIS A 277 REMARK 465 HIS A 278 REMARK 465 HIS A 279 REMARK 465 MET B 1 REMARK 465 ALA B 272 REMARK 465 ALA B 273 REMARK 465 HIS B 274 REMARK 465 HIS B 275 REMARK 465 HIS B 276 REMARK 465 HIS B 277 REMARK 465 HIS B 278 REMARK 465 HIS B 279 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE B 167 CG1 CG2 CD1 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 OD1 ASN B 161 O HOH B 416 1.89 REMARK 500 O HOH A 330 O HOH A 365 2.02 REMARK 500 O HOH B 428 O HOH B 475 2.09 REMARK 500 OE2 GLU B 267 O HOH B 444 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 84 CB CYS A 84 SG -0.102 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 ALA A 105 80.49 54.11 REMARK 500 LYS A 106 75.87 50.85 REMARK 500 ASN A 161 2.30 -68.02 REMARK 500 LYS A 168 -162.13 50.34 REMARK 500 SER A 169 -64.02 68.91 REMARK 500 SER A 178 107.74 -160.26 REMARK 500 TYR A 188 -15.14 -141.94 REMARK 500 ALA B 105 92.45 46.66 REMARK 500 LYS B 106 127.64 -21.57 REMARK 500 ASN B 161 8.29 -63.78 REMARK 500 LYS B 168 97.93 -48.92 REMARK 500 SER B 169 -78.84 -2.34 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 ILE A 166 ILE A 167 -149.63 REMARK 500 LYS A 168 SER A 169 -140.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 280 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DA3 RELATED DB: PDB REMARK 900 COLICIN M IN ANOTHER CRYSTAL FORM AT LOWER RESOLUTION DBREF 3DA4 A 1 271 UNP P05820 CEAM_ECOLX 1 271 DBREF 3DA4 B 1 271 UNP P05820 CEAM_ECOLX 1 271 SEQADV 3DA4 ALA A 272 UNP P05820 EXPRESSION TAG SEQADV 3DA4 ALA A 273 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 274 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 275 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 276 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 277 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 278 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS A 279 UNP P05820 EXPRESSION TAG SEQADV 3DA4 ALA B 272 UNP P05820 EXPRESSION TAG SEQADV 3DA4 ALA B 273 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 274 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 275 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 276 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 277 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 278 UNP P05820 EXPRESSION TAG SEQADV 3DA4 HIS B 279 UNP P05820 EXPRESSION TAG SEQRES 1 A 279 MET GLU THR LEU THR VAL HIS ALA PRO SER PRO SER THR SEQRES 2 A 279 ASN LEU PRO SER TYR GLY ASN GLY ALA PHE SER LEU SER SEQRES 3 A 279 ALA PRO HIS VAL PRO GLY ALA GLY PRO LEU LEU VAL GLN SEQRES 4 A 279 VAL VAL TYR SER PHE PHE GLN SER PRO ASN MET CYS LEU SEQRES 5 A 279 GLN ALA LEU THR GLN LEU GLU ASP TYR ILE LYS LYS HIS SEQRES 6 A 279 GLY ALA SER ASN PRO LEU THR LEU GLN ILE ILE SER THR SEQRES 7 A 279 ASN ILE GLY TYR PHE CYS ASN ALA ASP ARG ASN LEU VAL SEQRES 8 A 279 LEU HIS PRO GLY ILE SER VAL TYR ASP ALA TYR HIS PHE SEQRES 9 A 279 ALA LYS PRO ALA PRO SER GLN TYR ASP TYR ARG SER MET SEQRES 10 A 279 ASN MET LYS GLN MET SER GLY ASN VAL THR THR PRO ILE SEQRES 11 A 279 VAL ALA LEU ALA HIS TYR LEU TRP GLY ASN GLY ALA GLU SEQRES 12 A 279 ARG SER VAL ASN ILE ALA ASN ILE GLY LEU LYS ILE SER SEQRES 13 A 279 PRO MET LYS ILE ASN GLN ILE LYS ASP ILE ILE LYS SER SEQRES 14 A 279 GLY VAL VAL GLY THR PHE PRO VAL SER THR LYS PHE THR SEQRES 15 A 279 HIS ALA THR GLY ASP TYR ASN VAL ILE THR GLY ALA TYR SEQRES 16 A 279 LEU GLY ASN ILE THR LEU LYS THR GLU GLY THR LEU THR SEQRES 17 A 279 ILE SER ALA ASN GLY SER TRP THR TYR ASN GLY VAL VAL SEQRES 18 A 279 ARG SER TYR ASP ASP LYS TYR ASP PHE ASN ALA SER THR SEQRES 19 A 279 HIS ARG GLY ILE ILE GLY GLU SER LEU THR ARG LEU GLY SEQRES 20 A 279 ALA MET PHE SER GLY LYS GLU TYR GLN ILE LEU LEU PRO SEQRES 21 A 279 GLY GLU ILE HIS ILE LYS GLU SER GLY LYS ARG ALA ALA SEQRES 22 A 279 HIS HIS HIS HIS HIS HIS SEQRES 1 B 279 MET GLU THR LEU THR VAL HIS ALA PRO SER PRO SER THR SEQRES 2 B 279 ASN LEU PRO SER TYR GLY ASN GLY ALA PHE SER LEU SER SEQRES 3 B 279 ALA PRO HIS VAL PRO GLY ALA GLY PRO LEU LEU VAL GLN SEQRES 4 B 279 VAL VAL TYR SER PHE PHE GLN SER PRO ASN MET CYS LEU SEQRES 5 B 279 GLN ALA LEU THR GLN LEU GLU ASP TYR ILE LYS LYS HIS SEQRES 6 B 279 GLY ALA SER ASN PRO LEU THR LEU GLN ILE ILE SER THR SEQRES 7 B 279 ASN ILE GLY TYR PHE CYS ASN ALA ASP ARG ASN LEU VAL SEQRES 8 B 279 LEU HIS PRO GLY ILE SER VAL TYR ASP ALA TYR HIS PHE SEQRES 9 B 279 ALA LYS PRO ALA PRO SER GLN TYR ASP TYR ARG SER MET SEQRES 10 B 279 ASN MET LYS GLN MET SER GLY ASN VAL THR THR PRO ILE SEQRES 11 B 279 VAL ALA LEU ALA HIS TYR LEU TRP GLY ASN GLY ALA GLU SEQRES 12 B 279 ARG SER VAL ASN ILE ALA ASN ILE GLY LEU LYS ILE SER SEQRES 13 B 279 PRO MET LYS ILE ASN GLN ILE LYS ASP ILE ILE LYS SER SEQRES 14 B 279 GLY VAL VAL GLY THR PHE PRO VAL SER THR LYS PHE THR SEQRES 15 B 279 HIS ALA THR GLY ASP TYR ASN VAL ILE THR GLY ALA TYR SEQRES 16 B 279 LEU GLY ASN ILE THR LEU LYS THR GLU GLY THR LEU THR SEQRES 17 B 279 ILE SER ALA ASN GLY SER TRP THR TYR ASN GLY VAL VAL SEQRES 18 B 279 ARG SER TYR ASP ASP LYS TYR ASP PHE ASN ALA SER THR SEQRES 19 B 279 HIS ARG GLY ILE ILE GLY GLU SER LEU THR ARG LEU GLY SEQRES 20 B 279 ALA MET PHE SER GLY LYS GLU TYR GLN ILE LEU LEU PRO SEQRES 21 B 279 GLY GLU ILE HIS ILE LYS GLU SER GLY LYS ARG ALA ALA SEQRES 22 B 279 HIS HIS HIS HIS HIS HIS HET NO3 A 280 4 HET NO3 A 281 4 HET NO3 A 282 4 HET NO3 A 283 4 HET NO3 B 280 4 HETNAM NO3 NITRATE ION FORMUL 3 NO3 5(N O3 1-) FORMUL 8 HOH *641(H2 O) HELIX 1 1 SER A 17 ALA A 22 5 6 HELIX 2 2 LEU A 37 SER A 47 1 11 HELIX 3 3 SER A 47 GLY A 66 1 20 HELIX 4 4 ASN A 69 HIS A 93 1 25 HELIX 5 5 SER A 97 PHE A 104 1 8 HELIX 6 6 ALA A 108 TYR A 112 5 5 HELIX 7 7 ASP A 113 ASN A 118 1 6 HELIX 8 8 THR A 127 GLY A 139 1 13 HELIX 9 9 ILE A 148 ILE A 151 5 4 HELIX 10 10 SER A 156 ILE A 160 5 5 HELIX 11 11 ASN A 161 ILE A 167 1 7 HELIX 12 12 GLY A 186 TYR A 188 5 3 HELIX 13 13 ASN A 189 LEU A 196 1 8 HELIX 14 14 ARG A 236 PHE A 250 1 15 HELIX 15 15 SER B 17 ALA B 22 5 6 HELIX 16 16 LEU B 37 SER B 47 1 11 HELIX 17 17 SER B 47 GLY B 66 1 20 HELIX 18 18 ASN B 69 HIS B 93 1 25 HELIX 19 19 SER B 97 PHE B 104 1 8 HELIX 20 20 ALA B 108 TYR B 112 5 5 HELIX 21 21 ASP B 113 ASN B 118 1 6 HELIX 22 22 THR B 127 GLY B 139 1 13 HELIX 23 23 ILE B 148 ILE B 151 5 4 HELIX 24 24 SER B 156 ILE B 160 5 5 HELIX 25 25 ASN B 161 ILE B 167 1 7 HELIX 26 26 GLY B 186 TYR B 188 5 3 HELIX 27 27 ASN B 189 LEU B 196 1 8 HELIX 28 28 ARG B 236 PHE B 250 1 15 SHEET 1 A 4 GLN A 121 MET A 122 0 SHEET 2 A 4 ARG A 144 VAL A 146 1 O SER A 145 N MET A 122 SHEET 3 A 4 TYR A 255 LEU A 258 1 O LEU A 258 N ARG A 144 SHEET 4 A 4 LYS A 227 PHE A 230 -1 N PHE A 230 O TYR A 255 SHEET 1 B 4 GLY A 173 ALA A 184 0 SHEET 2 B 4 ASN A 198 ILE A 209 -1 O LEU A 207 N PHE A 175 SHEET 3 B 4 SER A 214 SER A 223 -1 O THR A 216 N THR A 208 SHEET 4 B 4 GLU A 262 LYS A 270 -1 O ILE A 265 N GLY A 219 SHEET 1 C 4 GLN B 121 MET B 122 0 SHEET 2 C 4 ARG B 144 VAL B 146 1 O SER B 145 N MET B 122 SHEET 3 C 4 TYR B 255 LEU B 258 1 O LEU B 258 N ARG B 144 SHEET 4 C 4 LYS B 227 PHE B 230 -1 N PHE B 230 O TYR B 255 SHEET 1 D 4 GLY B 173 ALA B 184 0 SHEET 2 D 4 ASN B 198 ILE B 209 -1 O LEU B 207 N PHE B 175 SHEET 3 D 4 SER B 214 SER B 223 -1 O ARG B 222 N LYS B 202 SHEET 4 D 4 GLU B 262 LYS B 270 -1 O GLU B 267 N TYR B 217 CISPEP 1 PHE A 104 ALA A 105 0 13.08 CISPEP 2 ALA A 105 LYS A 106 0 -7.22 CISPEP 3 LYS A 106 PRO A 107 0 -5.86 CISPEP 4 PHE B 104 ALA B 105 0 -2.58 CISPEP 5 ALA B 105 LYS B 106 0 18.08 CISPEP 6 LYS B 106 PRO B 107 0 -1.26 CISPEP 7 LYS B 168 SER B 169 0 18.20 SITE 1 AC1 7 MET A 119 LYS A 120 GLN A 121 HOH A 356 SITE 2 AC1 7 MET B 119 LYS B 120 GLN B 121 SITE 1 AC2 8 ARG A 88 LEU A 92 MET A 119 LYS B 120 SITE 2 AC2 8 GLN B 121 GLU B 143 ARG B 144 SER B 145 SITE 1 AC3 7 TYR A 18 SER A 24 LEU A 25 TYR A 82 SITE 2 AC3 7 TYR A 102 HOH A 368 HOH A 520 SITE 1 AC4 8 GLY A 66 ALA A 67 SER A 68 ASP A 229 SITE 2 AC4 8 GLU A 254 GLN A 256 HOH A 360 HOH A 400 SITE 1 AC5 9 LYS A 120 GLU A 143 ARG A 144 SER A 145 SITE 2 AC5 9 LEU A 258 ARG B 88 LEU B 92 MET B 119 SITE 3 AC5 9 HOH B 465 CRYST1 50.490 108.750 224.940 90.00 90.00 90.00 C 2 2 21 16 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 0.019806 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004446 0.00000