HEADER HYDROLASE 14-NOV-08 2W3T TITLE CHLORO COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-169; COMPND 5 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 6 EC: 3.5.1.31; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 ATCC: BAA-1025; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET20B(PLUS) KEYWDS PROTEIN BIOSYNTHESIS, IRON, NICKEL, HYDROLASE, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.T.NGO,G.J.PALM,W.HINRICHS REVDAT 5 13-DEC-23 2W3T 1 REMARK LINK REVDAT 4 06-MAR-19 2W3T 1 REMARK REVDAT 3 30-NOV-11 2W3T 1 JRNL REMARK REVDAT 2 13-JUL-11 2W3T 1 VERSN REVDAT 1 15-DEC-09 2W3T 0 JRNL AUTH N.T.H.YEN,X.BOGDANOVIC,G.J.PALM,O.KUHL,W.HINRICHS JRNL TITL STRUCTURE OF THE NI(II) COMPLEX OF ESCHERICHIA COLI PEPTIDE JRNL TITL 2 DEFORMYLASE AND SUGGESTIONS ON DEFORMYLASE ACTIVITIES JRNL TITL 3 DEPENDING ON DIFFERENT METAL(II) CENTRES. JRNL REF J.BIOL.INORG.CHEM. V. 15 195 2010 JRNL REFN ISSN 0949-8257 JRNL PMID 20112455 JRNL DOI 10.1007/S00775-009-0583-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BECKER,I.SCHLICHTING,W.KABSCH,D.GROCHE,S.SCHULTZ, REMARK 1 AUTH 2 A.F.WAGNER REMARK 1 TITL IRON CENTER, SUBSTRATE RECOGNITION AND MECHANISM OF PEPTIDE REMARK 1 TITL 2 DEFORMYLASE. REMARK 1 REF NAT.STRUCT.BIOL. V. 5 1053 1998 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 9846875 REMARK 1 DOI 10.1038/4162 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0047 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 17518 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1969 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4460 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.5280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1340 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 1.05000 REMARK 3 B33 (A**2) : -1.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.744 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1382 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1860 ; 1.078 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 172 ; 5.300 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;34.767 ;24.559 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 281 ;12.734 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.596 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 214 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1023 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 849 ; 0.389 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1380 ; 0.787 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 532 ; 1.564 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 479 ; 2.816 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 167 REMARK 3 RESIDUE RANGE : A 1001 A 1003 REMARK 3 RESIDUE RANGE : A 2112 A 2112 REMARK 3 RESIDUE RANGE : A 2140 A 2140 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1980 2.7420 15.5840 REMARK 3 T TENSOR REMARK 3 T11: 0.1272 T22: 0.0789 REMARK 3 T33: 0.0067 T12: -0.0103 REMARK 3 T13: -0.0087 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.9493 L22: 0.6131 REMARK 3 L33: 2.4501 L12: 0.0597 REMARK 3 L13: -0.4233 L23: -0.0362 REMARK 3 S TENSOR REMARK 3 S11: -0.0955 S12: 0.1209 S13: 0.0073 REMARK 3 S21: -0.0288 S22: 0.0497 S23: -0.0348 REMARK 3 S31: 0.0156 S32: 0.0754 S33: 0.0458 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. ONLY RESIDUAL U VALUES ARE SHOWN. CL A 1002 AND HOH A REMARK 3 1004 TO 1005 ALTERNATIVELY OCCUPY THE ACTIVE SITE HOH A A 1004 REMARK 3 AND HOH A 1005 HAVE BEEN REFINED WITH THE DISTANCE RESTRAINED TO REMARK 3 2.6 A REMARK 4 REMARK 4 2W3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MULTILAYER REMARK 200 OPTICS : OSMIC MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.290 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.74 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2A18 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.5% PEG4000, 100MM NAOAC PH 4.0, 293 REMARK 280 K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.04000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 A2051 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 168 REMARK 465 PRO A 169 REMARK 465 ASN A 170 REMARK 465 SER A 171 REMARK 465 SER A 172 REMARK 465 SER A 173 REMARK 465 VAL A 174 REMARK 465 ASP A 175 REMARK 465 LYS A 176 REMARK 465 LEU A 177 REMARK 465 ALA A 178 REMARK 465 ALA A 179 REMARK 465 ALA A 180 REMARK 465 LEU A 181 REMARK 465 GLU A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 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 PRO A 9 34.74 -97.90 REMARK 500 ASN A 24 -168.11 -121.16 REMARK 500 GLU A 95 -1.55 68.73 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 A2004 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A2021 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A2029 DISTANCE = 7.15 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 NI A1001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 90 SG REMARK 620 2 HIS A 132 NE2 114.5 REMARK 620 3 HIS A 136 NE2 101.8 106.4 REMARK 620 4 CL A1002 CL 112.5 106.2 115.6 REMARK 620 5 HOH A2140 O 144.7 94.2 88.5 35.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DEF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1 - 147), NMR, 9 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1LRU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXEDWITH REMARK 900 ANTIBIOTIC ACTINONIN REMARK 900 RELATED ID: 1BS8 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM IN COMPLEX WITH REMARK 900 TRIPEPTIDE MET-ALA-SER REMARK 900 RELATED ID: 1BSK RELATED DB: PDB REMARK 900 ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E. COLI REMARK 900 RELATED ID: 2VHM RELATED DB: PDB REMARK 900 STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME REMARK 900 RELATED ID: 1BS7 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM REMARK 900 RELATED ID: 2AI8 RELATED DB: PDB REMARK 900 E.COLI POLYPEPTIDE DEFORMYLASE COMPLEXED WITH SB-485343 REMARK 900 RELATED ID: 2DEF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1 - 147), NMR, 20 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1ICJ RELATED DB: PDB REMARK 900 PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM,COCRYSTALLIZED REMARK 900 WITH INHIBITOR POLYETHYLENE GLYCOL (PEG) REMARK 900 RELATED ID: 1BS4 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM ( NATIVE) IN COMPLEX REMARK 900 WITH INHIBITOR POLYETHYLENE GLYCOL REMARK 900 RELATED ID: 2W3U RELATED DB: PDB REMARK 900 FORMATE COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE REMARK 900 RELATED ID: 1BS5 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM REMARK 900 RELATED ID: 1BSZ RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM ( NATIVE) IN COMPLEX REMARK 900 WITH INHIBITOR POLYETHYLENE GLYCOL REMARK 900 RELATED ID: 1DFF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE REMARK 900 RELATED ID: 1G2A RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASECOMPLEXED WITH REMARK 900 ACTINONIN REMARK 900 RELATED ID: 1G27 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE DEFORMYLASECOMPLEXED WITH REMARK 900 THE INHIBITOR BB- 3497 REMARK 900 RELATED ID: 1BS6 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH REMARK 900 TRIPEPTIDE MET-ALA-SER REMARK 900 RELATED ID: 1BSJ RELATED DB: PDB REMARK 900 COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E. COLI REMARK 900 RELATED ID: 1DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 REMARK 900 RELATED ID: 2DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 DBREF 2W3T A 1 168 UNP P0A6K3 DEF_ECOLI 2 169 DBREF 2W3T A 169 188 PDB 2W3T 2W3T 169 188 SEQRES 1 A 188 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 A 188 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 A 188 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 A 188 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 A 188 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 A 188 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 A 188 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CYS LEU SEQRES 8 A 188 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 A 188 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 A 188 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 A 188 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 A 188 ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG GLN SEQRES 13 A 188 LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA PRO SEQRES 14 A 188 ASN SER SER SER VAL ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 15 A 188 HIS HIS HIS HIS HIS HIS HET NI A1001 1 HET CL A1002 1 HET EOH A1003 3 HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION HETNAM EOH ETHANOL FORMUL 2 NI NI 2+ FORMUL 3 CL CL 1- FORMUL 4 EOH C2 H6 O FORMUL 5 HOH *176(H2 O) HELIX 1 1 ASP A 10 LYS A 15 5 6 HELIX 2 2 ASN A 24 GLU A 41 1 18 HELIX 3 3 THR A 49 ASP A 52 5 4 HELIX 4 4 GLY A 124 VAL A 138 1 15 HELIX 5 5 LEU A 141 LEU A 146 5 6 HELIX 6 6 SER A 147 ALA A 166 1 20 SHEET 1 AA 5 GLY A 45 ALA A 47 0 SHEET 2 AA 5 ILE A 57 ILE A 60 -1 O VAL A 59 N LEU A 46 SHEET 3 AA 5 LEU A 70 SER A 81 -1 O LEU A 70 N ILE A 60 SHEET 4 AA 5 LYS A 105 LEU A 111 -1 O LYS A 105 N SER A 81 SHEET 5 AA 5 PRO A 117 ASP A 123 -1 O PHE A 118 N ALA A 110 SHEET 1 AB 2 THR A 84 GLU A 88 0 SHEET 2 AB 2 ALA A 98 ARG A 102 -1 O ALA A 98 N GLU A 88 LINK SG CYS A 90 NI NI A1001 1555 1555 2.34 LINK NE2 HIS A 132 NI NI A1001 1555 1555 2.10 LINK NE2 HIS A 136 NI NI A1001 1555 1555 2.09 LINK NI NI A1001 CL CL A1002 1555 1555 2.18 LINK NI NI A1001 O HOH A2140 1555 1555 1.95 CISPEP 1 ILE A 8 PRO A 9 0 7.25 SITE 1 AC1 6 GLN A 50 CYS A 90 HIS A 132 HIS A 136 SITE 2 AC1 6 CL A1002 HOH A2140 SITE 1 AC2 8 GLN A 50 LEU A 91 HIS A 132 GLU A 133 SITE 2 AC2 8 HIS A 136 NI A1001 HOH A2112 HOH A2140 SITE 1 AC3 5 GLY A 43 ILE A 44 GLY A 45 LEU A 91 SITE 2 AC3 5 HOH A2112 CRYST1 82.080 35.980 67.590 90.00 113.43 90.00 C 1 2 1 4 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 0.012183 0.000000 0.005280 0.00000 SCALE2 0.000000 0.027793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016125 0.00000