HEADER HYDROLASE/HYDROLASE INHIBITOR 16-APR-12 4EOX TITLE X-RAY STRUCTURE OF POLYPEPTIDE DEFORMYLASE BOUND TO A ACYLPROLINAMIDE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: P; 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: 171101; SOURCE 4 STRAIN: ATCC BAA-255 / R6; SOURCE 5 GENE: DEF, SPR1310; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-BETA, PEPTIDE DEFORMYLASE METAL ION BINDING, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.WARD,N.CAMPOBASSO REVDAT 3 28-FEB-24 4EOX 1 REMARK LINK REVDAT 2 02-JAN-13 4EOX 1 JRNL REVDAT 1 30-MAY-12 4EOX 0 JRNL AUTH J.M.AXTEN,J.R.MEDINA,C.W.BLACKLEDGE,C.DUQUENNE,S.W.GRANT, JRNL AUTH 2 M.A.BOBKO,T.PENG,W.H.MILLER,T.PINCKNEY,T.F.GALLAGHER, JRNL AUTH 3 S.KULKARNI,T.LEWANDOWSKI,G.S.VAN ALLER,R.ZONIS,P.WARD, JRNL AUTH 4 N.CAMPOBASSO JRNL TITL ACYLPROLINAMIDES: A NEW CLASS OF PEPTIDE DEFORMYLASE JRNL TITL 2 INHIBITORS WITH IN VIVO ANTIBACTERIAL ACTIVITY. JRNL REF BIOORG.MED.CHEM.LETT. V. 22 4028 2012 JRNL REFN ISSN 0960-894X JRNL PMID 22579486 JRNL DOI 10.1016/J.BMCL.2012.04.086 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_934) 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1092 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 49.7003 - 3.5661 1.00 2577 127 0.1642 0.2031 REMARK 3 2 3.5661 - 2.8306 1.00 2539 145 0.1880 0.2203 REMARK 3 3 2.8306 - 2.4728 1.00 2540 130 0.1931 0.2562 REMARK 3 4 2.4728 - 2.2467 1.00 2526 143 0.1825 0.2553 REMARK 3 5 2.2467 - 2.0857 1.00 2543 148 0.1801 0.2277 REMARK 3 6 2.0857 - 1.9627 1.00 2538 125 0.1841 0.2225 REMARK 3 7 1.9627 - 1.8644 1.00 2532 147 0.1911 0.2529 REMARK 3 8 1.8644 - 1.7832 1.00 2513 127 0.2293 0.2899 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 33.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.870 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) : 4.87990 REMARK 3 B22 (A**2) : 4.87990 REMARK 3 B33 (A**2) : -9.75970 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 : 0.019 1561 REMARK 3 ANGLE : 1.745 2107 REMARK 3 CHIRALITY : 0.132 238 REMARK 3 PLANARITY : 0.011 277 REMARK 3 DIHEDRAL : 14.820 593 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 4EOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000071889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND LAUE MONOCHROMATORS FROM REMARK 200 JJ X-RAY REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21449 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 92.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 2 M AMMONIUM SULFATE, 2% REMARK 280 PEG400, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 46.37400 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 69.56100 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 23.18700 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 465 GLU P 101 REMARK 465 GLU P 203 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 P 485 O HOH P 539 2.08 REMARK 500 O THR P 29 O HOH P 535 2.16 REMARK 500 O HOH P 514 O HOH P 525 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG P 146 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 P 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS P 130 SG REMARK 620 2 HIS P 173 NE2 109.2 REMARK 620 3 HIS P 177 NE2 87.0 101.9 REMARK 620 4 0S5 P 302 O1 93.5 103.1 153.3 REMARK 620 5 0S5 P 302 O30 151.6 98.0 95.4 72.0 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 P 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0S5 P 302 DBREF 4EOX P 1 203 UNP Q8DP79 DEF_STRR6 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 301 1 HET 0S5 P 302 30 HETNAM NI NICKEL (II) ION HETNAM 0S5 N-BENZOYL-1-[(2R)-3-CYCLOPENTYL-2-{[FORMYL(HYDROXY) HETNAM 2 0S5 AMINO]METHYL}PROPANOYL]-L-PROLINAMIDE FORMUL 2 NI NI 2+ FORMUL 3 0S5 C22 H29 N3 O5 FORMUL 4 HOH *153(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 MET P 109 N ILE P 85 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 301 1555 1555 2.45 LINK NE2 HIS P 173 NI NI P 301 1555 1555 2.25 LINK NE2 HIS P 177 NI NI P 301 1555 1555 2.11 LINK NI NI P 301 O1 0S5 P 302 1555 1555 2.03 LINK NI NI P 301 O30 0S5 P 302 1555 1555 2.23 CISPEP 1 PHE P 36 PRO P 37 0 8.46 SITE 1 AC1 5 GLN P 77 CYS P 130 HIS P 173 HIS P 177 SITE 2 AC1 5 0S5 P 302 SITE 1 AC2 16 ARG P 68 GLY P 69 GLY P 70 VAL P 71 SITE 2 AC2 16 GLY P 72 GLN P 77 GLY P 129 CYS P 130 SITE 3 AC2 16 LEU P 131 TYR P 166 HIS P 173 GLU P 174 SITE 4 AC2 16 HIS P 177 NI P 301 HOH P 530 HOH P 553 CRYST1 49.681 49.681 92.748 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 0.020128 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020128 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010782 0.00000