HEADER HYDROLASE 29-JUL-05 2AI7 TITLE S.PNEUMONIAE POLYPEPTIDE DEFORMYLASE COMPLEXED WITH SB-485345 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: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 STRAIN: ATCC BAA-255 R6; SOURCE 5 GENE: DEF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.SMITH,C.M.PETIT,K.AUBART,M.SMYTH,E.MCMANUS,J.JONES,A.FOSBERRY, AUTHOR 2 C.LEWIS,M.LONETTO,S.B.CHRISTENSEN REVDAT 3 14-FEB-24 2AI7 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2AI7 1 VERSN REVDAT 1 06-SEP-05 2AI7 0 JRNL AUTH K.J.SMITH,C.M.PETIT,K.AUBART,M.SMYTH,E.MCMANUS,J.JONES, JRNL AUTH 2 A.FOSBERRY,C.LEWIS,M.LONETTO,S.B.CHRISTENSEN JRNL TITL STRUCTURAL VARIATION AND INHIBITOR BINDING IN POLYPEPTIDE JRNL TITL 2 DEFORMYLASE FROM FOUR DIFFERENT BACTERIAL SPECIES JRNL REF PROTEIN SCI. V. 12 349 2003 JRNL REFN ISSN 0961-8368 JRNL PMID 12538898 JRNL DOI 10.1110/PS.0229303 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15032 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1521 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1519 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.74100 REMARK 3 B22 (A**2) : -4.74100 REMARK 3 B33 (A**2) : 9.48300 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 66.73 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER.PARAM REMARK 3 PARAMETER FILE 4 : PEG_MOD.PARAM REMARK 3 PARAMETER FILE 5 : SB4.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17182 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.22800 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 45.78250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.67375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.89125 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 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 MET A 0 REMARK 465 VAL A 92 REMARK 465 GLU A 93 REMARK 465 GLU A 94 REMARK 465 GLY A 95 REMARK 465 GLU A 96 REMARK 465 THR A 97 REMARK 465 PRO A 98 REMARK 465 GLN A 99 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 ARG A 135 158.58 174.79 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 A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 HIS A 173 NE2 118.6 REMARK 620 3 HIS A 177 NE2 96.6 102.4 REMARK 620 4 SB7 A 300 O22 85.4 113.2 138.2 REMARK 620 5 SB7 A 300 O25 140.9 100.0 80.1 73.0 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SB7 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AI8 RELATED DB: PDB REMARK 900 RELATED ID: 2AI9 RELATED DB: PDB REMARK 900 RELATED ID: 2AIA RELATED DB: PDB REMARK 900 RELATED ID: 2AIE RELATED DB: PDB DBREF 2AI7 A 0 202 UNP Q8DP79 DEF_STRR6 0 202 SEQADV 2AI7 SER A 7 UNP Q8DP79 THR 7 CONFLICT SEQADV 2AI7 CYS A 16 UNP Q8DP79 ASN 16 CONFLICT SEQADV 2AI7 SER A 25 UNP Q8DP79 THR 25 CONFLICT SEQRES 1 A 203 MET SER ALA ILE GLU ARG ILE SER LYS ALA ALA HIS LEU SEQRES 2 A 203 ILE ASP MET CYS ASP ILE ILE ARG GLU GLY ASN PRO SER SEQRES 3 A 203 LEU ARG THR VAL ALA GLU GLU VAL THR PHE PRO LEU SER SEQRES 4 A 203 ASP GLN GLU ILE ILE LEU GLY GLU LYS MET MET GLN PHE SEQRES 5 A 203 LEU LYS HIS SER GLN ASP PRO VAL MET ALA GLU LYS MET SEQRES 6 A 203 GLY LEU ARG GLY GLY VAL GLY LEU ALA ALA PRO GLN LEU SEQRES 7 A 203 ASP ILE SER LYS ARG ILE ILE ALA VAL LEU VAL PRO ASN SEQRES 8 A 203 ILE VAL GLU GLU GLY GLU THR PRO GLN GLU ALA TYR ASP SEQRES 9 A 203 LEU GLU ALA ILE MET TYR ASN PRO LYS ILE VAL SER HIS SEQRES 10 A 203 SER VAL GLN ASP ALA ALA LEU GLY GLU GLY GLU GLY CYS SEQRES 11 A 203 LEU SER VAL ASP ARG ASN VAL PRO GLY TYR VAL VAL ARG SEQRES 12 A 203 HIS ALA ARG VAL THR VAL ASP TYR PHE ASP LYS ASP GLY SEQRES 13 A 203 GLU LYS HIS ARG ILE LYS LEU LYS GLY TYR ASN SER ILE SEQRES 14 A 203 VAL VAL GLN HIS GLU ILE ASP HIS ILE ASN GLY ILE MET SEQRES 15 A 203 PHE TYR ASP ARG ILE ASN GLU LYS ASP PRO PHE ALA VAL SEQRES 16 A 203 LYS ASP GLY LEU LEU ILE LEU GLU HET NI A 301 1 HET SO4 A3001 5 HET SB7 A 300 13 HETNAM NI NICKEL (II) ION HETNAM SO4 SULFATE ION HETNAM SB7 [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL HETSYN SB7 SB-485345 FORMUL 2 NI NI 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 SB7 C10 H15 N O2 FORMUL 5 HOH *137(H2 O) HELIX 1 1 SER A 1 SER A 7 1 7 HELIX 2 2 ASP A 14 ILE A 18 5 5 HELIX 3 3 ASN A 23 THR A 28 5 6 HELIX 4 4 SER A 38 ASP A 57 1 20 HELIX 5 5 ASP A 57 MET A 64 1 8 HELIX 6 6 PRO A 75 ASP A 78 5 4 HELIX 7 7 LYS A 164 ILE A 178 1 15 HELIX 8 8 MET A 182 ILE A 187 5 6 SHEET 1 A 5 GLY A 71 ALA A 73 0 SHEET 2 A 5 ILE A 83 PRO A 89 -1 O ALA A 85 N LEU A 72 SHEET 3 A 5 TYR A 102 HIS A 116 -1 O ASP A 103 N VAL A 88 SHEET 4 A 5 VAL A 147 PHE A 152 -1 O ASP A 150 N LYS A 112 SHEET 5 A 5 LYS A 158 LEU A 163 -1 O HIS A 159 N TYR A 151 SHEET 1 B 3 ARG A 143 HIS A 144 0 SHEET 2 B 3 ASP A 120 LEU A 123 -1 N ALA A 121 O ARG A 143 SHEET 3 B 3 LEU A 199 LEU A 202 1 O LEU A 202 N ALA A 122 LINK SG CYS A 130 NI NI A 301 1555 1555 2.46 LINK NE2 HIS A 173 NI NI A 301 1555 1555 2.19 LINK NE2 HIS A 177 NI NI A 301 1555 1555 2.18 LINK O22 SB7 A 300 NI NI A 301 1555 1555 2.46 LINK O25 SB7 A 300 NI NI A 301 1555 1555 2.40 CISPEP 1 PHE A 35 PRO A 36 0 0.20 SITE 1 AC1 5 GLN A 76 CYS A 130 HIS A 173 HIS A 177 SITE 2 AC1 5 SB7 A 300 SITE 1 AC2 6 THR A 34 SER A 117 ARG A 146 HOH A3031 SITE 2 AC2 6 HOH A3087 HOH A3088 SITE 1 AC3 11 GLY A 71 GLN A 76 LEU A 123 GLU A 128 SITE 2 AC3 11 GLY A 129 CYS A 130 LEU A 131 HIS A 173 SITE 3 AC3 11 GLU A 174 HIS A 177 NI A 301 CRYST1 49.889 49.889 91.565 90.00 90.00 90.00 P 43 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 0.020044 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010921 0.00000