HEADER HYDROLASE 29-FEB-12 4AL3 TITLE PEPTIDE DEFORMYLASE (CO-FORM) WITH MERCAPTOETHANOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 STRAIN: BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET20B PLUS KEYWDS HYDROLASE, OXIDATION-REDUCTION EXPDTA X-RAY DIFFRACTION AUTHOR G.J.PALM,W.HINRICHS REVDAT 6 20-DEC-23 4AL3 1 REMARK LINK REVDAT 5 06-MAR-19 4AL3 1 REMARK LINK REVDAT 4 14-NOV-12 4AL3 1 JRNL REVDAT 3 31-OCT-12 4AL3 1 JRNL REVDAT 2 06-JUN-12 4AL3 1 TITLE REVDAT 1 04-APR-12 4AL3 0 JRNL AUTH M.STRIANESE,G.J.PALM,S.MILIONE,O.KUHL,W.HINRICHS, JRNL AUTH 2 C.PELLECCHIA JRNL TITL A FRET ENZYME-BASED PROBE FOR MONITORING HYDROGEN SULFIDE. JRNL REF INORG.CHEM. V. 51 11220 2012 JRNL REFN ISSN 0020-1669 JRNL PMID 23072298 JRNL DOI 10.1021/IC301363D REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.5 REMARK 3 NUMBER OF REFLECTIONS : 11804 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 : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 467 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1297 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.07000 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): 0.223 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.129 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1331 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 944 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1793 ; 1.401 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2313 ; 0.951 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 5.985 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 67 ;36.788 ;24.776 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 266 ;15.280 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.386 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 207 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1454 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 239 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 1 ;12.869 ; 5.000 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 : 2 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 146 REMARK 3 RESIDUE RANGE : A 1163 A 1165 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0520 -5.0470 31.3950 REMARK 3 T TENSOR REMARK 3 T11: 0.1493 T22: 0.1896 REMARK 3 T33: 0.1468 T12: 0.0101 REMARK 3 T13: 0.0674 T23: -0.1428 REMARK 3 L TENSOR REMARK 3 L11: 1.0036 L22: 3.3311 REMARK 3 L33: 7.4639 L12: 0.7696 REMARK 3 L13: -0.8639 L23: 2.9735 REMARK 3 S TENSOR REMARK 3 S11: 0.2838 S12: -0.0742 S13: 0.2074 REMARK 3 S21: 0.0248 S22: -0.6344 S23: 0.4954 REMARK 3 S31: -0.7189 S32: -0.9043 S33: 0.3507 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 147 A 164 REMARK 3 ORIGIN FOR THE GROUP (A): 2.7480 -16.6760 18.8560 REMARK 3 T TENSOR REMARK 3 T11: 0.3169 T22: 1.3169 REMARK 3 T33: 1.0735 T12: -0.1552 REMARK 3 T13: -0.3785 T23: -0.3702 REMARK 3 L TENSOR REMARK 3 L11: 16.4115 L22: 7.3772 REMARK 3 L33: 21.2321 L12: -1.2864 REMARK 3 L13: -9.9034 L23: 3.7590 REMARK 3 S TENSOR REMARK 3 S11: -0.3960 S12: 0.0923 S13: 0.7850 REMARK 3 S21: -1.1286 S22: -0.3727 S23: 2.5289 REMARK 3 S31: 0.7219 S32: -3.4642 S33: 0.7687 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. CO - BME S2 DISTANCE WAS RESTRAINED TO 2.30 ANGSTROM, REMARK 3 ESD 0.10 A. REMARK 4 REMARK 4 4AL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1290051461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.0.4 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13528 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 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 2W3T REMARK 200 REMARK 200 REMARK: REFLECTIONS FROM 2.30 - 2.21 A REMOVED BECAUSE OF ICE RING REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.5% PEG 4000, 100 MM NA-ACETATE PH REMARK 280 4.0, 293 K. TRANSFERRED TO 20% PEG, 50 MM ACETATE PH 6.0, THEN REMARK 280 SOAKED WITH 10 MM MERCAPTOETHANOL 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 76.44667 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 152.89333 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 114.67000 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 191.11667 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 38.22333 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 76.44667 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 152.89333 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 191.11667 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 114.67000 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 38.22333 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 ARG A 163 REMARK 465 LEU A 164 REMARK 465 LYS A 165 REMARK 465 ALA A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 SER A 169 REMARK 465 SER A 170 REMARK 465 SER A 171 REMARK 465 VAL A 172 REMARK 465 ASP A 173 REMARK 465 LYS A 174 REMARK 465 LEU A 175 REMARK 465 ALA A 176 REMARK 465 ALA A 177 REMARK 465 ALA A 178 REMARK 465 LEU A 179 REMARK 465 GLU A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 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 43.45 -95.73 REMARK 500 GLU A 42 31.84 71.19 REMARK 500 GLU A 95 -0.61 72.41 REMARK 500 LEU A 161 76.50 -102.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 COBALT (II) ION (CO): REPLACES NATIVE DIVALENT FE REMARK 600 BETA-MERCAPTOETHANOL (BME): BOUND TO CO AS THIOLATE 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 CO A1163 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CSO A 90 CB REMARK 620 2 CSO A 90 SG 28.0 REMARK 620 3 HIS A 132 NE2 90.3 113.3 REMARK 620 4 HIS A 136 NE2 132.7 107.9 107.5 REMARK 620 5 BME A1165 S2 107.2 114.2 103.4 110.4 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 CO A 1163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 1165 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 1BS7 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM 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: 1BSJ RELATED DB: PDB REMARK 900 COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI REMARK 900 RELATED ID: 1BSK RELATED DB: PDB REMARK 900 ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI 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: 1DEF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1 - 147), NMR, 9 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1DFF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE REMARK 900 RELATED ID: 1DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 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: 1G2A RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASECOMPLEXED WITH REMARK 900 ACTINONIN 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: 1LRU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXEDWITH REMARK 900 ANTIBIOTIC ACTINONIN REMARK 900 RELATED ID: 1XEM RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI ZINC-PEPTIDE REMARK 900 DEFORMYLASE BOUND TO FORMATE REMARK 900 RELATED ID: 1XEN RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF ESCHERICHIA COLI IRON-PEPTIDE REMARK 900 DEFORMYLASE BOUND TO FORMATE REMARK 900 RELATED ID: 1XEO RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTALS STRUCTURE OF COBALT- PEPTIDEDEFORMYLASE REMARK 900 BOUND TO FORMATE 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: 2DTF RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE:THIORPHAN DOCKING MODEL 1 REMARK 900 RELATED ID: 2VHM RELATED DB: PDB REMARK 900 STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME REMARK 900 RELATED ID: 2W3T RELATED DB: PDB REMARK 900 CHLORO COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE REMARK 900 RELATED ID: 2W3U RELATED DB: PDB REMARK 900 FORMATE COMPLEX OF THE NI-FORM OF E.COLI DEFORMYLASE REMARK 900 RELATED ID: 4AL2 RELATED DB: PDB REMARK 900 PEPTIDE DEFORMYLASE (NI-FORM) WITH HYDROSULFIDE DBREF 4AL3 A 1 168 UNP P0A6K3 DEF_ECOLI 2 169 SEQADV 4AL3 SER A 169 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 SER A 170 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 SER A 171 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 VAL A 172 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 ASP A 173 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 LYS A 174 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 LEU A 175 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 ALA A 176 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 ALA A 177 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 ALA A 178 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 LEU A 179 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 GLU A 180 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 181 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 182 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 183 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 184 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 185 UNP P0A6K3 EXPRESSION TAG SEQADV 4AL3 HIS A 186 UNP P0A6K3 EXPRESSION TAG SEQRES 1 A 186 SER VAL LEU GLN VAL LEU HIS ILE PRO ASP GLU ARG LEU SEQRES 2 A 186 ARG LYS VAL ALA LYS PRO VAL GLU GLU VAL ASN ALA GLU SEQRES 3 A 186 ILE GLN ARG ILE VAL ASP ASP MET PHE GLU THR MET TYR SEQRES 4 A 186 ALA GLU GLU GLY ILE GLY LEU ALA ALA THR GLN VAL ASP SEQRES 5 A 186 ILE HIS GLN ARG ILE ILE VAL ILE ASP VAL SER GLU ASN SEQRES 6 A 186 ARG ASP GLU ARG LEU VAL LEU ILE ASN PRO GLU LEU LEU SEQRES 7 A 186 GLU LYS SER GLY GLU THR GLY ILE GLU GLU GLY CSO LEU SEQRES 8 A 186 SER ILE PRO GLU GLN ARG ALA LEU VAL PRO ARG ALA GLU SEQRES 9 A 186 LYS VAL LYS ILE ARG ALA LEU ASP ARG ASP GLY LYS PRO SEQRES 10 A 186 PHE GLU LEU GLU ALA ASP GLY LEU LEU ALA ILE CYS ILE SEQRES 11 A 186 GLN HIS GLU MET ASP HIS LEU VAL GLY LYS LEU PHE MET SEQRES 12 A 186 ASP TYR LEU SER PRO LEU LYS GLN GLN ARG ILE ARG GLN SEQRES 13 A 186 LYS VAL GLU LYS LEU ASP ARG LEU LYS ALA ARG ALA SER SEQRES 14 A 186 SER SER VAL ASP LYS LEU ALA ALA ALA LEU GLU HIS HIS SEQRES 15 A 186 HIS HIS HIS HIS MODRES 4AL3 CSO A 90 CYS S-HYDROXYCYSTEINE HET CSO A 90 7 HET CO A1163 1 HET CL A1164 1 HET BME A1165 4 HETNAM CSO S-HYDROXYCYSTEINE HETNAM CO COBALT (II) ION HETNAM CL CHLORIDE ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 CO CO 2+ FORMUL 3 CL CL 1- FORMUL 4 BME C2 H6 O S FORMUL 5 HOH *98(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 GLU A 159 1 13 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 C GLY A 89 N CSO A 90 1555 1555 1.33 LINK C CSO A 90 N LEU A 91 1555 1555 1.34 LINK CB CSO A 90 CO CO A1163 1555 1555 3.35 LINK SG CSO A 90 CO CO A1163 1555 1555 2.15 LINK NE2 HIS A 132 CO CO A1163 1555 1555 2.09 LINK NE2 HIS A 136 CO CO A1163 1555 1555 2.31 LINK CO CO A1163 S2 BME A1165 1555 1555 2.19 CISPEP 1 ILE A 8 PRO A 9 0 4.68 SITE 1 AC1 5 GLN A 50 CSO A 90 HIS A 132 HIS A 136 SITE 2 AC1 5 BME A1165 SITE 1 AC2 1 HIS A 132 SITE 1 AC3 10 GLY A 43 ILE A 44 GLY A 45 GLN A 50 SITE 2 AC3 10 CSO A 90 LEU A 91 HIS A 132 GLU A 133 SITE 3 AC3 10 HIS A 136 CO A1163 CRYST1 55.630 55.630 229.340 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 0.017976 0.010378 0.000000 0.00000 SCALE2 0.000000 0.020757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004360 0.00000