HEADER HYDROLASE 10-MAR-22 7U9B TITLE CRYSTAL STRUCTURE OF INDOLINE 7 WITH KPC-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC-1; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLA, KPC, KPC1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BETA-LACTAMASE, TETRAZOLE, INHIBITOR, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.AKHTAR,Y.CHEN REVDAT 3 06-NOV-24 7U9B 1 REMARK REVDAT 2 25-OCT-23 7U9B 1 REMARK REVDAT 1 15-MAR-23 7U9B 0 JRNL AUTH K.DEFREES,E.M.CAMBEIS,Y.CHEN,A.R.RENSLO JRNL TITL PROBING THE BINDING HOT SPOTS OF KPC-2 CARBAPENEMASE USING JRNL TITL 2 REVERSIBLE TETRAZOLE-BASED INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19324 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 926 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 36.0500 - 3.7291 1.00 2756 161 0.1655 0.2061 REMARK 3 2 3.7291 - 2.9603 1.00 2654 128 0.1674 0.2168 REMARK 3 3 2.9603 - 2.5862 1.00 2614 145 0.1797 0.2116 REMARK 3 4 2.5862 - 2.3498 1.00 2606 120 0.1815 0.2359 REMARK 3 5 2.3498 - 2.1814 1.00 2600 118 0.1895 0.2880 REMARK 3 6 2.1814 - 2.0528 1.00 2590 125 0.2006 0.2547 REMARK 3 7 2.0528 - 1.9500 1.00 2578 129 0.2213 0.2872 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.44 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7U9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000262927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 36.055 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.72300 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 2.8.3 REMARK 200 STARTING MODEL: 3C5A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 5%(V/V) ETHANOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.45500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.33000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.45500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.33000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. 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 A 498 O HOH A 502 2.15 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 SER A 53 -22.16 -146.38 REMARK 500 CYS A 69 -145.76 49.19 REMARK 500 TRP A 105 68.94 60.35 REMARK 500 ARG A 220 -114.12 -119.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 7U9B A 25 293 UNP Q9F663 BLKPC_KLEPN 25 291 SEQADV 7U9B MET A 24 UNP Q9F663 INITIATING METHIONINE SEQRES 1 A 268 MET LEU THR ASN LEU VAL ALA GLU PRO PHE ALA LYS LEU SEQRES 2 A 268 GLU GLN ASP PHE GLY GLY SER ILE GLY VAL TYR ALA MET SEQRES 3 A 268 ASP THR GLY SER GLY ALA THR VAL SER TYR ARG ALA GLU SEQRES 4 A 268 GLU ARG PHE PRO LEU CYS SER SER PHE LYS GLY PHE LEU SEQRES 5 A 268 ALA ALA ALA VAL LEU ALA ARG SER GLN GLN GLN ALA GLY SEQRES 6 A 268 LEU LEU ASP THR PRO ILE ARG TYR GLY LYS ASN ALA LEU SEQRES 7 A 268 VAL PRO TRP SER PRO ILE SER GLU LYS TYR LEU THR THR SEQRES 8 A 268 GLY MET THR VAL ALA GLU LEU SER ALA ALA ALA VAL GLN SEQRES 9 A 268 TYR SER ASP ASN ALA ALA ALA ASN LEU LEU LEU LYS GLU SEQRES 10 A 268 LEU GLY GLY PRO ALA GLY LEU THR ALA PHE MET ARG SER SEQRES 11 A 268 ILE GLY ASP THR THR PHE ARG LEU ASP ARG TRP GLU LEU SEQRES 12 A 268 GLU LEU ASN SER ALA ILE PRO GLY ASP ALA ARG ASP THR SEQRES 13 A 268 SER SER PRO ARG ALA VAL THR GLU SER LEU GLN LYS LEU SEQRES 14 A 268 THR LEU GLY SER ALA LEU ALA ALA PRO GLN ARG GLN GLN SEQRES 15 A 268 PHE VAL ASP TRP LEU LYS GLY ASN THR THR GLY ASN HIS SEQRES 16 A 268 ARG ILE ARG ALA ALA VAL PRO ALA ASP TRP ALA VAL GLY SEQRES 17 A 268 ASP LYS THR GLY THR CYS GLY VAL TYR GLY THR ALA ASN SEQRES 18 A 268 ASP TYR ALA VAL VAL TRP PRO THR GLY ARG ALA PRO ILE SEQRES 19 A 268 VAL LEU ALA VAL TYR THR ARG ALA PRO ASN LYS ASP ASP SEQRES 20 A 268 LYS HIS SER GLU ALA VAL ILE ALA ALA ALA ALA ARG LEU SEQRES 21 A 268 ALA LEU GLU GLY LEU GLY VAL ASN HET M2I A 301 26 HETNAM M2I [(3S)-3-(1H-TETRAZOL-5-YL)-2,3-DIHYDRO-1H-INDOL-1- HETNAM 2 M2I YL][3-(TRIFLUOROMETHYL)PHENYL]METHANONE FORMUL 2 M2I C17 H12 F3 N5 O FORMUL 3 HOH *112(H2 O) HELIX 1 AA1 MET A 24 GLY A 41 1 18 HELIX 2 AA2 SER A 71 GLN A 85 1 15 HELIX 3 AA3 GLY A 89 ASP A 92 5 4 HELIX 4 AA4 GLY A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 LEU A 113 5 6 HELIX 6 AA6 VAL A 119 SER A 130 1 12 HELIX 7 AA7 ASP A 131 GLY A 143 1 13 HELIX 8 AA8 GLY A 143 ILE A 155 1 13 HELIX 9 AA9 LEU A 167 SER A 171 5 5 HELIX 10 AB1 SER A 182 LEU A 195 1 14 HELIX 11 AB2 ALA A 200 GLY A 213 1 14 HELIX 12 AB3 ARG A 220 VAL A 225 5 6 HELIX 13 AB4 SER A 275 LEU A 290 1 16 SHEET 1 AA1 5 THR A 56 TYR A 60 0 SHEET 2 AA1 5 SER A 43 ASP A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 AA1 5 ILE A 259 ARG A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 AA1 5 ALA A 244 TRP A 251 -1 N VAL A 250 O ILE A 259 SHEET 5 AA1 5 ALA A 230 THR A 237 -1 N GLY A 236 O ASN A 245 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 AA3 2 PRO A 94 ILE A 95 0 SHEET 2 AA3 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.05 CISPEP 1 GLU A 166 LEU A 167 0 4.18 CRYST1 56.710 58.910 76.660 90.00 90.00 90.00 P 2 21 21 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 0.017634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016975 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013045 0.00000