HEADER HYDROLASE 14-NOV-08 2W3U TITLE FORMATE 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 HYDROLASE, NICKEL, FORMATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.T.NGO,G.J.PALM,W.HINRICHS REVDAT 6 13-DEC-23 2W3U 1 REMARK LINK REVDAT 5 06-MAR-19 2W3U 1 REMARK REVDAT 4 19-FEB-14 2W3U 1 REMARK REVDAT 3 30-NOV-11 2W3U 1 JRNL REMARK ATOM REVDAT 2 13-JUL-11 2W3U 1 VERSN REVDAT 1 15-DEC-09 2W3U 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 13594 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 641 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 39.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.75000 REMARK 3 B22 (A**2) : 1.75000 REMARK 3 B33 (A**2) : -2.63000 REMARK 3 B12 (A**2) : 0.88000 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): 0.217 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.185 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.285 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1359 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1830 ; 1.452 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 5.638 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;31.967 ;24.559 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 277 ;15.196 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.435 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 211 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1007 ; 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): 832 ; 0.578 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1351 ; 1.035 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 527 ; 2.109 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 477 ; 3.481 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 165 REMARK 3 RESIDUE RANGE : A 1001 A 1002 REMARK 3 ORIGIN FOR THE GROUP (A): 15.8040 -6.2100 30.2110 REMARK 3 T TENSOR REMARK 3 T11: 0.2237 T22: 0.4164 REMARK 3 T33: 0.2770 T12: 0.0089 REMARK 3 T13: 0.0767 T23: -0.1715 REMARK 3 L TENSOR REMARK 3 L11: 1.7589 L22: 4.2650 REMARK 3 L33: 9.8437 L12: 0.5661 REMARK 3 L13: -1.7429 L23: 3.4086 REMARK 3 S TENSOR REMARK 3 S11: 0.3482 S12: 0.2367 S13: 0.1772 REMARK 3 S21: 0.0647 S22: -0.8125 S23: 0.6484 REMARK 3 S31: -0.8418 S32: -1.5525 S33: 0.4643 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. REMARK 4 REMARK 4 2W3U 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_1290038116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 4.1 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 : NULL 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 : 14750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 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 (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.370 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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 1XEO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 0.2M (NH4)2SO4, 0.1M REMARK 280 NAOAC PH 4.1, 293 K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 76.20333 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 152.40667 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 114.30500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 190.50833 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 38.10167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.20333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 152.40667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 190.50833 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 114.30500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 38.10167 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 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 166 REMARK 465 ARG A 167 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: 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 A 2013 O HOH A 2055 1.97 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 ASP A 10 112.90 -29.57 REMARK 500 GLU A 21 -74.88 -75.24 REMARK 500 HIS A 54 64.86 -100.30 REMARK 500 REMARK 500 REMARK: NULL 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 120.1 REMARK 620 3 HIS A 136 NE2 103.8 111.6 REMARK 620 4 FMT A1002 O1 116.1 107.6 94.5 REMARK 620 N 1 2 3 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 FMT A 1002 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: 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: 2W3T RELATED DB: PDB REMARK 900 CHLORO COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE 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: 1DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 REMARK 900 RELATED ID: 1BSJ RELATED DB: PDB REMARK 900 COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E. COLI REMARK 900 RELATED ID: 2DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 DBREF 2W3U A 1 168 UNP P0A6K3 DEF_ECOLI 2 169 DBREF 2W3U A 169 188 PDB 2W3U 2W3U 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 FMT A1002 3 HETNAM NI NICKEL (II) ION HETNAM FMT FORMIC ACID FORMUL 2 NI NI 2+ FORMUL 3 FMT C H2 O2 FORMUL 4 HOH *96(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 ASP A 123 VAL A 138 1 16 HELIX 5 5 LEU A 141 LEU A 146 5 6 HELIX 6 6 SER A 147 LYS A 165 1 19 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 ALA A 122 -1 O PHE A 118 N ALA A 110 SHEET 1 AB 2 GLU A 87 GLU A 88 0 SHEET 2 AB 2 ALA A 98 LEU A 99 -1 O ALA A 98 N GLU A 88 LINK SG CYS A 90 NI NI A1001 1555 1555 2.18 LINK NE2 HIS A 132 NI NI A1001 1555 1555 2.05 LINK NE2 HIS A 136 NI NI A1001 1555 1555 2.04 LINK NI NI A1001 O1 FMT A1002 1555 1555 2.02 CISPEP 1 ILE A 8 PRO A 9 0 5.50 SITE 1 AC1 5 GLN A 50 CYS A 90 HIS A 132 HIS A 136 SITE 2 AC1 5 FMT A1002 SITE 1 AC2 10 GLY A 45 GLN A 50 CYS A 90 LEU A 91 SITE 2 AC2 10 HIS A 132 GLU A 133 HIS A 136 NI A1001 SITE 3 AC2 10 HOH A2095 HOH A2096 CRYST1 54.590 54.590 228.610 90.00 90.00 120.00 P 61 2 2 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 0.018318 0.010576 0.000000 0.00000 SCALE2 0.000000 0.021152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004374 0.00000