HEADER HYDROLASE/HYDROLASE INHIBITOR 09-MAR-22 7U8S TITLE CRYSTAL STRUCTURE OF KPC-2 WITH COMPOUND 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, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.AKHTAR,Y.CHEN REVDAT 2 25-OCT-23 7U8S 1 REMARK REVDAT 1 22-MAR-23 7U8S 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 35065 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2001 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 47.4600 - 3.8600 1.00 2539 158 0.1877 0.1994 REMARK 3 2 3.8500 - 3.0600 1.00 2432 144 0.1901 0.2128 REMARK 3 3 3.0600 - 2.6700 1.00 2385 148 0.2027 0.2494 REMARK 3 4 2.6700 - 2.4300 0.98 2339 142 0.1988 0.2426 REMARK 3 5 2.4300 - 2.2600 1.00 2364 145 0.2079 0.2494 REMARK 3 6 2.2600 - 2.1200 1.00 2361 142 0.1937 0.2373 REMARK 3 7 2.1200 - 2.0200 1.00 2348 136 0.1976 0.2009 REMARK 3 8 2.0200 - 1.9300 1.00 2334 145 0.2042 0.2323 REMARK 3 9 1.9300 - 1.8500 0.99 2318 135 0.2056 0.2501 REMARK 3 10 1.8500 - 1.7900 0.99 2324 150 0.2202 0.2711 REMARK 3 11 1.7900 - 1.7300 0.99 2335 134 0.2235 0.2792 REMARK 3 12 1.7300 - 1.6800 1.00 2303 139 0.2401 0.3057 REMARK 3 13 1.6800 - 1.6400 1.00 2348 142 0.2534 0.2890 REMARK 3 14 1.6400 - 1.6000 1.00 2334 141 0.2627 0.2835 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.60 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 7U8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000262847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-20 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 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 : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 59.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 7.9000 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) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : 0.52600 REMARK 200 FOR SHELL : 1.400 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 (%): 47.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 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 29.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.83000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.83000 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 452 LIES ON A SPECIAL POSITION. 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 THR A 26 REMARK 465 ASN A 27 REMARK 465 LEU A 28 REMARK 465 VAL A 29 REMARK 465 ALA A 30 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 86 CG CD OE1 NE2 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 478 O HOH A 501 2.16 REMARK 500 O HOH A 406 O HOH A 522 2.18 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 CYS A 69 -142.20 47.62 REMARK 500 TRP A 105 76.93 54.65 REMARK 500 ARG A 220 -120.74 -112.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 7U8S A 26 292 UNP Q9F663 BLKPC_KLEPN 26 290 SEQRES 1 A 265 THR ASN LEU VAL ALA GLU PRO PHE ALA LYS LEU GLU GLN SEQRES 2 A 265 ASP PHE GLY GLY SER ILE GLY VAL TYR ALA MET ASP THR SEQRES 3 A 265 GLY SER GLY ALA THR VAL SER TYR ARG ALA GLU GLU ARG SEQRES 4 A 265 PHE PRO LEU CYS SER SER PHE LYS GLY PHE LEU ALA ALA SEQRES 5 A 265 ALA VAL LEU ALA ARG SER GLN GLN GLN ALA GLY LEU LEU SEQRES 6 A 265 ASP THR PRO ILE ARG TYR GLY LYS ASN ALA LEU VAL PRO SEQRES 7 A 265 TRP SER PRO ILE SER GLU LYS TYR LEU THR THR GLY MET SEQRES 8 A 265 THR VAL ALA GLU LEU SER ALA ALA ALA VAL GLN TYR SER SEQRES 9 A 265 ASP ASN ALA ALA ALA ASN LEU LEU LEU LYS GLU LEU GLY SEQRES 10 A 265 GLY PRO ALA GLY LEU THR ALA PHE MET ARG SER ILE GLY SEQRES 11 A 265 ASP THR THR PHE ARG LEU ASP ARG TRP GLU LEU GLU LEU SEQRES 12 A 265 ASN SER ALA ILE PRO GLY ASP ALA ARG ASP THR SER SER SEQRES 13 A 265 PRO ARG ALA VAL THR GLU SER LEU GLN LYS LEU THR LEU SEQRES 14 A 265 GLY SER ALA LEU ALA ALA PRO GLN ARG GLN GLN PHE VAL SEQRES 15 A 265 ASP TRP LEU LYS GLY ASN THR THR GLY ASN HIS ARG ILE SEQRES 16 A 265 ARG ALA ALA VAL PRO ALA ASP TRP ALA VAL GLY ASP LYS SEQRES 17 A 265 THR GLY THR CYS GLY VAL TYR GLY THR ALA ASN ASP TYR SEQRES 18 A 265 ALA VAL VAL TRP PRO THR GLY ARG ALA PRO ILE VAL LEU SEQRES 19 A 265 ALA VAL TYR THR ARG ALA PRO ASN LYS ASP ASP LYS HIS SEQRES 20 A 265 SER GLU ALA VAL ILE ALA ALA ALA ALA ARG LEU ALA LEU SEQRES 21 A 265 GLU GLY LEU GLY VAL HET LW0 A 301 24 HETNAM LW0 3-FLUORO-N-[(1R,3S)-3-(1H-TETRAZOL-5-YL)-2,3-DIHYDRO- HETNAM 2 LW0 1H-INDEN-1-YL]BENZAMIDE FORMUL 2 LW0 C17 H14 F N5 O FORMUL 3 HOH *148(H2 O) HELIX 1 AA1 GLU A 31 GLY A 41 1 11 HELIX 2 AA2 SER A 71 GLN A 85 1 15 HELIX 3 AA3 GLY A 98 LEU A 102 5 5 HELIX 4 AA4 ILE A 108 LEU A 113 5 6 HELIX 5 AA5 VAL A 119 SER A 130 1 12 HELIX 6 AA6 ASP A 131 LEU A 142 1 12 HELIX 7 AA7 GLY A 143 ILE A 155 1 13 HELIX 8 AA8 LEU A 167 SER A 171 5 5 HELIX 9 AA9 SER A 182 LEU A 195 1 14 HELIX 10 AB1 ALA A 200 GLY A 213 1 14 HELIX 11 AB2 ARG A 220 VAL A 225 1 6 HELIX 12 AB3 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 ALA A 230 O TRP A 251 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 2.06 CISPEP 1 GLU A 166 LEU A 167 0 4.95 CRYST1 56.060 59.950 77.660 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 0.017838 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012877 0.00000