HEADER HYDROLASE/HYDROLASE INHIBITOR 13-JUL-11 3SW8 TITLE STREP PEPTIDE DEFORMYLASE WITH A TIME DEPENDENT DICHLOROBENZAMIDE- TITLE 2 REVERSE HYDROXAMIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE 3; COMPND 3 CHAIN: P; COMPND 4 SYNONYM: PDF 3, POLYPEPTIDE DEFORMYLASE 3; 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 GENE: DEFB, DEF3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-BETA, PEPTIDE DEFORMYLASE, METAL BINDING PROTEIN, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CAMPOBASSO,K.J.SMITH REVDAT 4 28-FEB-24 3SW8 1 REMARK LINK REVDAT 3 16-APR-14 3SW8 1 REMARK REVDAT 2 17-AUG-11 3SW8 1 JRNL REVDAT 1 27-JUL-11 3SW8 0 JRNL AUTH R.TOTORITIS,C.DURAISWAMI,A.N.TAYLOR,J.J.KERRIGAN, JRNL AUTH 2 N.CAMPOBASSO,K.J.SMITH,P.WARD,B.W.KING,M.MURRAYZ-THOMPSON, JRNL AUTH 3 A.D.JONES,G.S.VAN ALLER,K.M.AUBART,M.ZALACAIN,S.H.THRALL, JRNL AUTH 4 T.D.MEEK,B.SCHWARTZ JRNL TITL UNDERSTANDING THE ORIGINS OF TIME-DEPENDENT INHIBITION BY JRNL TITL 2 POLYPEPTIDE DEFORMYLASE INHIBITORS. JRNL REF BIOCHEMISTRY V. 50 6642 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21711014 JRNL DOI 10.1021/BI200655G REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.J.SMITH,C.M.PETIT,K.AUBART,M.SMYTH,E.MCMANUS,J.JONES, REMARK 1 AUTH 2 A.FOSBERRY,C.LEWIS,M.LONETTO,S.B.CHRISTENSEN REMARK 1 TITL STRUCTURAL VARIATION AND INHIBITOR BINDING IN POLYPEPTIDE REMARK 1 TITL 2 DEFORMYLASE FROM FOUR DIFFERENT BACTERIAL SPECIES. REMARK 1 REF PROTEIN SCI. V. 12 349 2003 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 12538898 REMARK 1 DOI 10.1110/PS.0229303 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 23920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.1271 - 4.0963 0.99 1644 147 0.1840 0.2071 REMARK 3 2 4.0963 - 3.2539 0.99 1611 147 0.1767 0.1919 REMARK 3 3 3.2539 - 2.8433 1.00 1618 142 0.1960 0.2051 REMARK 3 4 2.8433 - 2.5836 1.00 1602 147 0.2083 0.2139 REMARK 3 5 2.5836 - 2.3986 0.99 1604 139 0.1911 0.2341 REMARK 3 6 2.3986 - 2.2573 0.98 1579 134 0.1928 0.2577 REMARK 3 7 2.2573 - 2.1444 0.98 1593 145 0.1931 0.2596 REMARK 3 8 2.1444 - 2.0511 0.99 1610 140 0.1947 0.2334 REMARK 3 9 2.0511 - 1.9721 0.98 1580 137 0.1988 0.2608 REMARK 3 10 1.9721 - 1.9041 0.97 1547 140 0.2026 0.2567 REMARK 3 11 1.9041 - 1.8446 0.95 1548 132 0.1934 0.2353 REMARK 3 12 1.8446 - 1.7919 0.95 1510 135 0.2059 0.2559 REMARK 3 13 1.7919 - 1.7447 0.93 1520 132 0.2248 0.2245 REMARK 3 14 1.7447 - 1.7020 0.89 1414 123 0.2469 0.2826 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.76 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.19310 REMARK 3 B22 (A**2) : 3.19310 REMARK 3 B33 (A**2) : -6.38620 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1576 REMARK 3 ANGLE : 1.040 2128 REMARK 3 CHIRALITY : 0.072 238 REMARK 3 PLANARITY : 0.005 279 REMARK 3 DIHEDRAL : 13.026 591 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 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 : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 - 2.8 M AMMONIUM SULFATE, 1 % - 3 REMARK 280 % PEG400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 45.80250 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 68.70375 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 22.90125 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: P 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 P 1 REMARK 465 VAL P 93 REMARK 465 GLU P 94 REMARK 465 GLU P 95 REMARK 465 GLY P 96 REMARK 465 GLU P 97 REMARK 465 THR P 98 REMARK 465 PRO P 99 REMARK 465 GLN P 100 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 P 204 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS P 130 SG REMARK 620 2 HIS P 173 NE2 110.1 REMARK 620 3 HIS P 177 NE2 94.7 96.6 REMARK 620 4 5LI P 205 O13 157.1 91.9 88.7 REMARK 620 5 5LI P 205 O15 88.5 120.9 138.6 74.4 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 NI P 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5LI P 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 207 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3STR RELATED DB: PDB REMARK 900 RELATED ID: 3SVJ RELATED DB: PDB DBREF 3SW8 P 1 203 UNP Q939R9 Q939R9_STRPN 1 203 SEQRES 1 P 203 MET SER ALA ILE GLU ARG ILE THR LYS ALA ALA HIS LEU SEQRES 2 P 203 ILE ASP MET ASN ASP ILE ILE ARG GLU GLY ASN PRO THR SEQRES 3 P 203 LEU ARG THR VAL ALA GLU GLU VAL THR PHE PRO LEU SER SEQRES 4 P 203 ASP GLN GLU ILE ILE LEU GLY GLU LYS MET MET GLN PHE SEQRES 5 P 203 LEU LYS HIS SER GLN ASP PRO VAL MET ALA GLU LYS MET SEQRES 6 P 203 GLY LEU ARG GLY GLY VAL GLY LEU ALA ALA PRO GLN LEU SEQRES 7 P 203 ASP ILE SER LYS ARG ILE ILE ALA VAL LEU VAL PRO ASN SEQRES 8 P 203 ILE VAL GLU GLU GLY GLU THR PRO GLN GLU ALA TYR ASP SEQRES 9 P 203 LEU GLU ALA ILE MET TYR ASN PRO LYS ILE VAL SER HIS SEQRES 10 P 203 SER VAL GLN ASP ALA ALA LEU GLY GLU GLY GLU GLY CYS SEQRES 11 P 203 LEU SER VAL ASP ARG ASN VAL PRO GLY TYR VAL VAL ARG SEQRES 12 P 203 HIS ALA ARG VAL THR VAL ASP TYR PHE ASP LYS ASP GLY SEQRES 13 P 203 GLU LYS HIS ARG ILE LYS LEU LYS GLY TYR ASN SER ILE SEQRES 14 P 203 VAL VAL GLN HIS GLU ILE ASP HIS ILE ASN GLY ILE MET SEQRES 15 P 203 PHE TYR ASP ARG ILE ASN GLU LYS ASP PRO PHE ALA VAL SEQRES 16 P 203 LYS ASP GLY LEU LEU ILE LEU GLU HET NI P 204 1 HET SO4 P3001 5 HET 5LI P 205 17 HET SO4 P 206 5 HET SO4 P 207 5 HETNAM NI NICKEL (II) ION HETNAM SO4 SULFATE ION HETNAM 5LI 2,3-DICHLORO-N-{2-[FORMYL(HYDROXY)AMINO]ETHYL}BENZAMIDE FORMUL 2 NI NI 2+ FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 5LI C10 H10 CL2 N2 O3 FORMUL 7 HOH *168(H2 O) HELIX 1 1 SER P 2 THR P 8 1 7 HELIX 2 2 ASP P 15 ILE P 19 5 5 HELIX 3 3 ASN P 24 THR P 29 5 6 HELIX 4 4 SER P 39 GLN P 57 1 19 HELIX 5 5 ASP P 58 GLY P 66 1 9 HELIX 6 6 PRO P 76 ASP P 79 5 4 HELIX 7 7 LYS P 164 ASN P 179 1 16 HELIX 8 8 MET P 182 ILE P 187 5 6 SHEET 1 A 5 GLY P 72 ALA P 74 0 SHEET 2 A 5 ILE P 84 PRO P 90 -1 O ALA P 86 N LEU P 73 SHEET 3 A 5 TYR P 103 HIS P 117 -1 O LEU P 105 N VAL P 89 SHEET 4 A 5 VAL P 147 PHE P 152 -1 O THR P 148 N VAL P 115 SHEET 5 A 5 LYS P 158 LEU P 163 -1 O HIS P 159 N TYR P 151 SHEET 1 B 3 ARG P 143 HIS P 144 0 SHEET 2 B 3 ASP P 121 LEU P 124 -1 N ALA P 122 O ARG P 143 SHEET 3 B 3 LEU P 199 LEU P 202 1 O LEU P 202 N ALA P 123 LINK SG CYS P 130 NI NI P 204 1555 1555 2.46 LINK NE2 HIS P 173 NI NI P 204 1555 1555 2.34 LINK NE2 HIS P 177 NI NI P 204 1555 1555 2.21 LINK NI NI P 204 O13 5LI P 205 1555 1555 2.17 LINK NI NI P 204 O15 5LI P 205 1555 1555 2.28 CISPEP 1 PHE P 36 PRO P 37 0 5.25 SITE 1 AC1 5 GLN P 77 CYS P 130 HIS P 173 HIS P 177 SITE 2 AC1 5 5LI P 205 SITE 1 AC2 6 THR P 35 SER P 118 ARG P 146 HOH P 237 SITE 2 AC2 6 HOH P 343 HOH P 371 SITE 1 AC3 15 GLY P 70 VAL P 71 GLY P 72 GLN P 77 SITE 2 AC3 15 LEU P 124 GLU P 128 GLY P 129 CYS P 130 SITE 3 AC3 15 LEU P 131 ILE P 169 VAL P 170 HIS P 173 SITE 4 AC3 15 GLU P 174 HIS P 177 NI P 204 SITE 1 AC4 3 ALA P 107 ILE P 108 HOH P 300 SITE 1 AC5 4 HIS P 144 ARG P 186 HOH P 346 HOH P 354 CRYST1 50.015 50.015 91.605 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 0.019994 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019994 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010916 0.00000