HEADER HYDROLASE/HYDROLASE INHIBITOR 09-MAY-19 6OW2 TITLE X-RAY STRUCTURE OF POLYPEPTIDE DEFORMYLASE 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: 1313; SOURCE 4 GENE: DEFB, DEF, DEF_1, DEF_2, DEF_3, A5N45_09745, ERS019420_01538, SOURCE 5 ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, SOURCE 6 ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_01588, SOURCE 7 ERS409327_03241, ERS409593_03947, KK0981_34260, NCTC12140_00964; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, METAL PROTEIN, ENZYME, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CAMPOBASSO,J.SPLETSTOSER,P.WARD REVDAT 3 13-MAR-24 6OW2 1 REMARK REVDAT 2 21-AUG-19 6OW2 1 JRNL REVDAT 1 26-JUN-19 6OW2 0 JRNL AUTH J.T.SPLETSTOSER,J.DREABIT,A.N.KNOX,A.BENOWITZ,N.CAMPOBASSO, JRNL AUTH 2 P.WARD,G.CUI,T.LEWANDOWSKI,L.MCCLOSKEY,K.M.AUBART JRNL TITL DISCOVERY OF PIPERAZIC ACID PEPTIDE DEFORMYLASE INHIBITORS JRNL TITL 2 WITH IN VIVO ACTIVITY FOR RESPIRATORY TRACT AND SKIN JRNL TITL 3 INFECTIONS. JRNL REF BIOORG.MED.CHEM.LETT. V. 29 2410 2019 JRNL REFN ESSN 1464-3405 JRNL PMID 31160176 JRNL DOI 10.1016/J.BMCL.2019.05.028 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 24688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1251 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 33.8600 - 3.5400 1.00 2668 142 0.1656 0.1790 REMARK 3 2 3.5400 - 2.8100 1.00 2639 153 0.2017 0.2365 REMARK 3 3 2.8100 - 2.4500 1.00 2628 144 0.2169 0.2248 REMARK 3 4 2.4500 - 2.2300 1.00 2642 118 0.2119 0.2473 REMARK 3 5 2.2300 - 2.0700 1.00 2648 130 0.2028 0.2167 REMARK 3 6 2.0700 - 1.9500 1.00 2613 139 0.2059 0.2572 REMARK 3 7 1.9500 - 1.8500 0.99 2605 148 0.2262 0.2602 REMARK 3 8 1.8500 - 1.7700 0.99 2558 154 0.2283 0.2907 REMARK 3 9 1.7700 - 1.7000 0.92 2436 123 0.2467 0.2759 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.204 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.066 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1558 REMARK 3 ANGLE : 0.796 2104 REMARK 3 CHIRALITY : 0.056 237 REMARK 3 PLANARITY : 0.005 271 REMARK 3 DIHEDRAL : 8.960 947 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 6OW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 175 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 : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 91.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 % - 4 % PEG400 40% - 56% AMMONIUM REMARK 280 SULFATE 0.1 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 45.74100 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 68.61150 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 22.87050 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ILE P 92 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 401 O HOH P 429 2.07 REMARK 500 OD1 ASP P 104 O HOH P 401 2.08 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 P 134 56.68 -100.07 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 118.6 REMARK 620 3 HIS P 177 NE2 93.7 99.6 REMARK 620 4 NB4 P 302 N18 119.0 92.3 134.0 REMARK 620 5 NB4 P 302 O19 90.2 107.9 146.3 28.8 REMARK 620 6 NB4 P 302 O21 152.6 88.6 83.7 52.1 77.7 REMARK 620 N 1 2 3 4 5 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 NB4 P 302 DBREF 6OW2 P 2 203 UNP Q939R9 Q939R9_STREE 2 203 SEQRES 1 P 202 SER ALA ILE GLU ARG ILE THR LYS ALA ALA HIS LEU ILE SEQRES 2 P 202 ASP MET ASN ASP ILE ILE ARG GLU GLY ASN PRO THR LEU SEQRES 3 P 202 ARG THR VAL ALA GLU GLU VAL THR PHE PRO LEU SER ASP SEQRES 4 P 202 GLN GLU ILE ILE LEU GLY GLU LYS MET MET GLN PHE LEU SEQRES 5 P 202 LYS HIS SER GLN ASP PRO VAL MET ALA GLU LYS MET GLY SEQRES 6 P 202 LEU ARG GLY GLY VAL GLY LEU ALA ALA PRO GLN LEU ASP SEQRES 7 P 202 ILE SER LYS ARG ILE ILE ALA VAL LEU VAL PRO ASN ILE SEQRES 8 P 202 VAL GLU GLU GLY GLU THR PRO GLN GLU ALA TYR ASP LEU SEQRES 9 P 202 GLU ALA ILE MET TYR ASN PRO LYS ILE VAL SER HIS SER SEQRES 10 P 202 VAL GLN ASP ALA ALA LEU GLY GLU GLY GLU GLY CYS LEU SEQRES 11 P 202 SER VAL ASP ARG ASN VAL PRO GLY TYR VAL VAL ARG HIS SEQRES 12 P 202 ALA ARG VAL THR VAL ASP TYR PHE ASP LYS ASP GLY GLU SEQRES 13 P 202 LYS HIS ARG ILE LYS LEU LYS GLY TYR ASN SER ILE VAL SEQRES 14 P 202 VAL GLN HIS GLU ILE ASP HIS ILE ASN GLY ILE MET PHE SEQRES 15 P 202 TYR ASP ARG ILE ASN GLU LYS ASP PRO PHE ALA VAL LYS SEQRES 16 P 202 ASP GLY LEU LEU ILE LEU GLU HET NI P 301 1 HET NB4 P 302 66 HETNAM NI NICKEL (II) ION HETNAM NB4 (2R)-2-(CYCLOPENTYLMETHYL)-N'-{5-FLUORO-6-[(9AS)- HETNAM 2 NB4 HEXAHYDROPYRAZINO[2,1-C][1,4]OXAZIN-8(1H)-YL]-2- HETNAM 3 NB4 METHYLPYRIMIDIN-4-YL}-3-[HYDROXY(HYDROXYMETHYL) HETNAM 4 NB4 AMINO]PROPANEHYDRAZIDE FORMUL 2 NI NI 2+ FORMUL 3 NB4 C22 H36 F N7 O4 FORMUL 4 HOH *86(H2 O) HELIX 1 AA1 SER P 2 THR P 8 1 7 HELIX 2 AA2 ASP P 15 ILE P 19 5 5 HELIX 3 AA3 ASN P 24 THR P 29 5 6 HELIX 4 AA4 SER P 39 ASP P 58 1 20 HELIX 5 AA5 ASP P 58 GLY P 66 1 9 HELIX 6 AA6 PRO P 76 ASP P 79 5 4 HELIX 7 AA7 LYS P 164 ASN P 179 1 16 HELIX 8 AA8 MET P 182 ILE P 187 5 6 SHEET 1 AA1 5 GLY P 72 ALA P 74 0 SHEET 2 AA1 5 ILE P 84 VAL P 89 -1 O ALA P 86 N LEU P 73 SHEET 3 AA1 5 LEU P 105 HIS P 117 -1 O MET P 109 N ILE P 85 SHEET 4 AA1 5 VAL P 147 PHE P 152 -1 O ASP P 150 N LYS P 113 SHEET 5 AA1 5 LYS P 158 LEU P 163 -1 O HIS P 159 N TYR P 151 SHEET 1 AA2 3 ARG P 143 HIS P 144 0 SHEET 2 AA2 3 ASP P 121 LEU P 124 -1 N ALA P 122 O ARG P 143 SHEET 3 AA2 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 2.39 LINK NE2 HIS P 173 NI NI P 301 1555 1555 2.16 LINK NE2 HIS P 177 NI NI P 301 1555 1555 2.04 LINK NI NI P 301 N18 NB4 P 302 1555 1555 2.74 LINK NI NI P 301 O19 NB4 P 302 1555 1555 1.95 LINK NI NI P 301 O21 NB4 P 302 1555 1555 2.33 CISPEP 1 PHE P 36 PRO P 37 0 4.99 SITE 1 AC1 5 GLN P 77 CYS P 130 HIS P 173 HIS P 177 SITE 2 AC1 5 NB4 P 302 SITE 1 AC2 16 GLN P 57 GLY P 69 GLY P 70 VAL P 71 SITE 2 AC2 16 GLY P 72 GLN P 77 GLU P 128 GLY P 129 SITE 3 AC2 16 CYS P 130 LEU P 131 HIS P 173 GLU P 174 SITE 4 AC2 16 HIS P 177 LYS P 190 NI P 301 HOH P 434 CRYST1 50.334 50.334 91.482 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 0.019867 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019867 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010931 0.00000