HEADER HYDROLASE 11-MAR-22 7UA7 TITLE CRYSTAL STRUCTURE OF INDOLINE 9 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 2 25-OCT-23 7UA7 1 REMARK REVDAT 1 15-MAR-23 7UA7 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 12251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1230 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 46.5400 - 4.6734 1.00 1354 161 0.1764 0.2204 REMARK 3 2 4.6734 - 3.7099 1.00 1293 141 0.1507 0.2164 REMARK 3 3 3.7099 - 3.2411 1.00 1277 140 0.1705 0.2120 REMARK 3 4 3.2411 - 2.9448 1.00 1255 138 0.2019 0.2455 REMARK 3 5 2.9448 - 2.7338 1.00 1256 137 0.1935 0.2309 REMARK 3 6 2.7338 - 2.5726 1.00 1244 141 0.1847 0.2195 REMARK 3 7 2.5726 - 2.4438 0.98 1219 137 0.1840 0.2701 REMARK 3 8 2.4438 - 2.3374 0.91 1128 120 0.1839 0.2782 REMARK 3 9 2.3374 - 2.2474 0.80 995 115 0.1957 0.2588 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.24 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 7UA7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000263013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-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 : 19-BM 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12678 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.247 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 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 (%): 46.22 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 29.37350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.14500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.37350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.14500 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 453 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 LYS A 73 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 NH1 ARG A 266 O HOH A 401 2.11 REMARK 500 O3 GOL A 303 O HOH A 402 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 SER A 22 -64.07 62.24 REMARK 500 CYS A 69 -138.04 50.69 REMARK 500 ARG A 220 -113.16 -117.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UA7 A 25 294 UNP Q9F663 BLKPC_KLEPN 25 292 SEQADV 7UA7 GLY A 21 UNP Q9F663 EXPRESSION TAG SEQADV 7UA7 SER A 22 UNP Q9F663 EXPRESSION TAG SEQADV 7UA7 HIS A 23 UNP Q9F663 EXPRESSION TAG SEQADV 7UA7 MET A 24 UNP Q9F663 EXPRESSION TAG SEQRES 1 A 272 GLY SER HIS MET LEU THR ASN LEU VAL ALA GLU PRO PHE SEQRES 2 A 272 ALA LYS LEU GLU GLN ASP PHE GLY GLY SER ILE GLY VAL SEQRES 3 A 272 TYR ALA MET ASP THR GLY SER GLY ALA THR VAL SER TYR SEQRES 4 A 272 ARG ALA GLU GLU ARG PHE PRO LEU CYS SER SER PHE LYS SEQRES 5 A 272 GLY PHE LEU ALA ALA ALA VAL LEU ALA ARG SER GLN GLN SEQRES 6 A 272 GLN ALA GLY LEU LEU ASP THR PRO ILE ARG TYR GLY LYS SEQRES 7 A 272 ASN ALA LEU VAL PRO TRP SER PRO ILE SER GLU LYS TYR SEQRES 8 A 272 LEU THR THR GLY MET THR VAL ALA GLU LEU SER ALA ALA SEQRES 9 A 272 ALA VAL GLN TYR SER ASP ASN ALA ALA ALA ASN LEU LEU SEQRES 10 A 272 LEU LYS GLU LEU GLY GLY PRO ALA GLY LEU THR ALA PHE SEQRES 11 A 272 MET ARG SER ILE GLY ASP THR THR PHE ARG LEU ASP ARG SEQRES 12 A 272 TRP GLU LEU GLU LEU ASN SER ALA ILE PRO GLY ASP ALA SEQRES 13 A 272 ARG ASP THR SER SER PRO ARG ALA VAL THR GLU SER LEU SEQRES 14 A 272 GLN LYS LEU THR LEU GLY SER ALA LEU ALA ALA PRO GLN SEQRES 15 A 272 ARG GLN GLN PHE VAL ASP TRP LEU LYS GLY ASN THR THR SEQRES 16 A 272 GLY ASN HIS ARG ILE ARG ALA ALA VAL PRO ALA ASP TRP SEQRES 17 A 272 ALA VAL GLY ASP LYS THR GLY THR CYS GLY VAL TYR GLY SEQRES 18 A 272 THR ALA ASN ASP TYR ALA VAL VAL TRP PRO THR GLY ARG SEQRES 19 A 272 ALA PRO ILE VAL LEU ALA VAL TYR THR ARG ALA PRO ASN SEQRES 20 A 272 LYS ASP ASP LYS HIS SER GLU ALA VAL ILE ALA ALA ALA SEQRES 21 A 272 ALA ARG LEU ALA LEU GLU GLY LEU GLY VAL ASN GLY HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HET M53 A 304 37 HETNAM GOL GLYCEROL HETNAM M53 TERT-BUTYL {(3R)-3-[(1H-TETRAZOL-5-YL)CARBAMOYL]-1-[3- HETNAM 2 M53 (TRIFLUOROMETHYL)BENZOYL]-2,3-DIHYDRO-1H-INDOL-3- HETNAM 3 M53 YL}CARBAMATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 M53 C23 H22 F3 N7 O4 FORMUL 6 HOH *80(H2 O) HELIX 1 AA1 HIS A 23 VAL A 29 1 7 HELIX 2 AA2 VAL A 29 GLY A 41 1 13 HELIX 3 AA3 CYS A 69 PHE A 72 5 4 HELIX 4 AA4 GLY A 74 GLY A 74 5 1 HELIX 5 AA5 PHE A 75 GLN A 87 1 13 HELIX 6 AA6 GLY A 98 LEU A 102 5 5 HELIX 7 AA7 ILE A 108 LEU A 113 5 6 HELIX 8 AA8 VAL A 119 SER A 130 1 12 HELIX 9 AA9 ASP A 131 GLY A 143 1 13 HELIX 10 AB1 GLY A 144 ILE A 155 1 12 HELIX 11 AB2 LEU A 167 SER A 171 5 5 HELIX 12 AB3 SER A 182 LEU A 195 1 14 HELIX 13 AB4 ALA A 200 GLY A 213 1 14 HELIX 14 AB5 ILE A 221 VAL A 225 5 5 HELIX 15 AB6 SER A 275 GLY A 291 1 17 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 ASP A 246 O VAL A 263 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 2.04 CISPEP 1 GLU A 166 LEU A 167 0 6.93 CRYST1 56.844 58.747 76.290 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 0.017592 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013108 0.00000