HEADER HYDROLASE-INHIBITOR 04-FEB-23 8I8F TITLE CRYSTAL STRUCTURE OF NDM-1 AT PH5.5 (SUCCINATE) IN COMPLEX WITH TITLE 2 HYDROLYZED COMPOUND 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO BETA LACTAMASE NDM-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METALLO BETA-LACTAMASE,METALLO-BETA-LACTAMASE NDM1, COMPND 5 METALLOBETALACTAMASE NDM-1,NDM-1,NDM1 METALLO-BETA-LACTAMASE,NEW COMPND 6 DELHI METALLO CARBAPENEMASE-1,NEW DELHI METALLO-BETA-LACTAMASE NDM-1, COMPND 7 NEW DELHI METALLO-BETA-LACTAMSE 1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLANDM-1, BLA NDM-1, BLANDM1, NDM-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PENICILLIN, HYDROLASE-INHIBITOR COMPLEX, HYDROLASE-INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR X.SHI,W.LIU REVDAT 2 28-FEB-24 8I8F 1 JRNL REVDAT 1 07-FEB-24 8I8F 0 JRNL AUTH X.SHI,Y.DAI,Z.LAN,S.WANG,L.CUI,C.XIAO,K.ZHAO,X.LI,W.LIU, JRNL AUTH 2 Q.ZHANG JRNL TITL INTERPLAY BETWEEN THE BETA-LACTAM SIDE CHAIN AND AN JRNL TITL 2 ACTIVE-SITE MOBILE LOOP OF NDM-1 IN PENICILLIN HYDROLYSIS AS JRNL TITL 3 A POTENTIAL TARGET FOR MECHANISM-BASED INHIBITOR DESIGN. JRNL REF INT.J.BIOL.MACROMOL. V. 262 30041 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 38336327 JRNL DOI 10.1016/J.IJBIOMAC.2024.130041 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 33742 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1738 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 27.7700 - 4.3200 1.00 2889 150 0.1409 0.1586 REMARK 3 2 4.3100 - 3.4300 1.00 2782 141 0.1278 0.1489 REMARK 3 3 3.4300 - 2.9900 1.00 2692 164 0.1415 0.1758 REMARK 3 4 2.9900 - 2.7200 1.00 2696 146 0.1610 0.2107 REMARK 3 5 2.7200 - 2.5300 1.00 2697 133 0.1625 0.1962 REMARK 3 6 2.5300 - 2.3800 1.00 2679 140 0.1653 0.2106 REMARK 3 7 2.3800 - 2.2600 1.00 2652 158 0.1589 0.2378 REMARK 3 8 2.2600 - 2.1600 1.00 2652 145 0.1593 0.2380 REMARK 3 9 2.1600 - 2.0800 1.00 2642 156 0.1636 0.1889 REMARK 3 10 2.0800 - 2.0000 1.00 2664 154 0.1586 0.2168 REMARK 3 11 2.0000 - 1.9400 1.00 2654 140 0.1689 0.1986 REMARK 3 12 1.9400 - 1.8900 0.87 2305 111 0.1980 0.2879 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) : 0.153 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.79 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 : 0.007 3761 REMARK 3 ANGLE : 0.946 5140 REMARK 3 CHIRALITY : 0.059 571 REMARK 3 PLANARITY : 0.007 708 REMARK 3 DIHEDRAL : 6.331 568 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4393 2.0685 -22.1401 REMARK 3 T TENSOR REMARK 3 T11: 0.3145 T22: 0.2359 REMARK 3 T33: 0.2333 T12: 0.0558 REMARK 3 T13: -0.0489 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 0.1245 L22: 0.1547 REMARK 3 L33: 0.0936 L12: 0.0099 REMARK 3 L13: -0.0323 L23: -0.0281 REMARK 3 S TENSOR REMARK 3 S11: 0.1201 S12: 0.3941 S13: -0.1013 REMARK 3 S21: -0.3904 S22: -0.1103 S23: 0.1996 REMARK 3 S31: 0.3961 S32: 0.1222 S33: -0.0051 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.3698 6.8631 -23.1604 REMARK 3 T TENSOR REMARK 3 T11: 0.2178 T22: 0.2079 REMARK 3 T33: 0.1917 T12: -0.0092 REMARK 3 T13: -0.0769 T23: -0.0556 REMARK 3 L TENSOR REMARK 3 L11: 0.2383 L22: 0.1953 REMARK 3 L33: 0.2429 L12: 0.1060 REMARK 3 L13: -0.1488 L23: -0.2014 REMARK 3 S TENSOR REMARK 3 S11: -0.1843 S12: 0.2442 S13: -0.1177 REMARK 3 S21: -0.2887 S22: -0.1477 S23: 0.2169 REMARK 3 S31: 0.1629 S32: -0.1985 S33: -0.2636 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0217 18.0899 -14.8507 REMARK 3 T TENSOR REMARK 3 T11: 0.0942 T22: 0.1024 REMARK 3 T33: 0.0735 T12: -0.0048 REMARK 3 T13: -0.0137 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.5238 L22: 0.9946 REMARK 3 L33: 0.5079 L12: -0.0015 REMARK 3 L13: 0.1023 L23: -0.0517 REMARK 3 S TENSOR REMARK 3 S11: 0.0296 S12: 0.0019 S13: -0.0097 REMARK 3 S21: 0.0004 S22: -0.0218 S23: 0.0050 REMARK 3 S31: 0.0356 S32: 0.0188 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 256 THROUGH 270 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2937 26.1757 -31.1468 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.2317 REMARK 3 T33: 0.1515 T12: 0.0046 REMARK 3 T13: 0.0139 T23: 0.0421 REMARK 3 L TENSOR REMARK 3 L11: 0.0170 L22: 0.0514 REMARK 3 L33: 0.0267 L12: 0.0156 REMARK 3 L13: 0.0161 L23: 0.0116 REMARK 3 S TENSOR REMARK 3 S11: 0.0564 S12: 0.3395 S13: 0.2789 REMARK 3 S21: -0.2775 S22: -0.1632 S23: -0.1427 REMARK 3 S31: -0.3660 S32: 0.1346 S33: -0.0016 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 32 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4614 24.6018 -48.3412 REMARK 3 T TENSOR REMARK 3 T11: 0.3192 T22: 0.2690 REMARK 3 T33: 0.2178 T12: -0.0487 REMARK 3 T13: -0.0202 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.1649 L22: 0.1777 REMARK 3 L33: 0.5940 L12: 0.0640 REMARK 3 L13: -0.0384 L23: -0.0947 REMARK 3 S TENSOR REMARK 3 S11: -0.1353 S12: -0.3692 S13: 0.0251 REMARK 3 S21: 0.4221 S22: -0.1722 S23: -0.1492 REMARK 3 S31: -0.2058 S32: 0.3621 S33: -0.0243 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 58 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1896 19.5379 -43.8250 REMARK 3 T TENSOR REMARK 3 T11: 0.1993 T22: 0.2705 REMARK 3 T33: 0.1651 T12: -0.0577 REMARK 3 T13: 0.0094 T23: -0.0799 REMARK 3 L TENSOR REMARK 3 L11: 0.6809 L22: 0.1864 REMARK 3 L33: 0.0650 L12: -0.0828 REMARK 3 L13: 0.2075 L23: -0.0356 REMARK 3 S TENSOR REMARK 3 S11: 0.0695 S12: -0.5638 S13: 0.2866 REMARK 3 S21: 0.2165 S22: -0.2592 S23: 0.0903 REMARK 3 S31: -0.1234 S32: -0.1846 S33: -0.1378 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 71 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.8874 19.7236 -56.1605 REMARK 3 T TENSOR REMARK 3 T11: 0.1244 T22: 0.0946 REMARK 3 T33: 0.1471 T12: 0.0235 REMARK 3 T13: 0.0100 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 0.4550 L22: 0.1428 REMARK 3 L33: 0.1396 L12: 0.1155 REMARK 3 L13: -0.0382 L23: -0.1423 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: 0.0112 S13: 0.2695 REMARK 3 S21: -0.0125 S22: 0.0107 S23: 0.0450 REMARK 3 S31: -0.1122 S32: -0.0395 S33: 0.0296 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 119 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2213 4.7870 -52.6019 REMARK 3 T TENSOR REMARK 3 T11: 0.0930 T22: 0.0969 REMARK 3 T33: 0.1094 T12: 0.0102 REMARK 3 T13: -0.0132 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.3396 L22: 0.7339 REMARK 3 L33: 0.2882 L12: 0.0116 REMARK 3 L13: -0.1084 L23: 0.0008 REMARK 3 S TENSOR REMARK 3 S11: 0.0166 S12: 0.0031 S13: 0.0685 REMARK 3 S21: 0.0387 S22: -0.0093 S23: -0.1132 REMARK 3 S31: -0.0077 S32: 0.0089 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 256 THROUGH 270 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.3132 0.2548 -43.2076 REMARK 3 T TENSOR REMARK 3 T11: 0.1696 T22: 0.1994 REMARK 3 T33: 0.2317 T12: 0.0046 REMARK 3 T13: -0.0456 T23: 0.0332 REMARK 3 L TENSOR REMARK 3 L11: 0.0375 L22: 0.6474 REMARK 3 L33: 0.1044 L12: 0.1266 REMARK 3 L13: -0.0292 L23: 0.0511 REMARK 3 S TENSOR REMARK 3 S11: 0.0316 S12: -0.1633 S13: -0.0079 REMARK 3 S21: 0.4040 S22: -0.0142 S23: -0.2029 REMARK 3 S31: 0.2237 S32: 0.1016 S33: -0.0129 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 8I8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33742 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 27.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 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 1.19.1_4122 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SUCCINATE PH5.5, 32%PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 19.55700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.76700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.42350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.76700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.55700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.42350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A 1 REMARK 465 GLU A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 MET A 7 REMARK 465 HIS A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 LEU A 13 REMARK 465 SER A 14 REMARK 465 THR A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 LEU A 21 REMARK 465 MET A 22 REMARK 465 LEU A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 CYS A 26 REMARK 465 MET A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LEU B 3 REMARK 465 PRO B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 MET B 7 REMARK 465 HIS B 8 REMARK 465 PRO B 9 REMARK 465 VAL B 10 REMARK 465 ALA B 11 REMARK 465 LYS B 12 REMARK 465 LEU B 13 REMARK 465 SER B 14 REMARK 465 THR B 15 REMARK 465 ALA B 16 REMARK 465 LEU B 17 REMARK 465 ALA B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 LEU B 21 REMARK 465 MET B 22 REMARK 465 LEU B 23 REMARK 465 SER B 24 REMARK 465 GLY B 25 REMARK 465 CYS B 26 REMARK 465 MET B 27 REMARK 465 PRO B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 30 REMARK 465 ILE B 31 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 403 O HOH A 593 1.71 REMARK 500 OE2 GLU A 227 O HOH A 401 1.72 REMARK 500 O HOH B 556 O HOH B 617 1.77 REMARK 500 O HOH A 454 O HOH A 543 1.78 REMARK 500 NH1 ARG B 264 O HOH B 401 1.79 REMARK 500 OD2 ASP B 95 O HOH B 402 1.81 REMARK 500 O ILE A 31 O HOH A 402 1.82 REMARK 500 O HOH A 507 O HOH A 619 1.83 REMARK 500 O HOH A 579 O HOH A 597 1.84 REMARK 500 OH TYR B 64 O HOH B 403 1.89 REMARK 500 O HOH A 485 O HOH A 505 1.92 REMARK 500 N ARG B 32 O HOH B 404 1.98 REMARK 500 O HOH A 539 O HOH A 590 2.01 REMARK 500 N GLY A 84 O HOH A 403 2.01 REMARK 500 OD2 ASP A 223 O HOH A 404 2.05 REMARK 500 O HOH A 413 O HOH A 666 2.07 REMARK 500 O HOH A 602 O HOH A 623 2.11 REMARK 500 OE1 GLU A 227 O HOH A 405 2.13 REMARK 500 O HOH B 631 O HOH B 666 2.16 REMARK 500 OH TYR A 64 O HOH A 406 2.16 REMARK 500 OE2 GLU A 152 O HOH A 404 2.16 REMARK 500 O HOH B 410 O HOH B 458 2.17 REMARK 500 O HOH A 562 O HOH A 635 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 596 O HOH B 647 3554 1.88 REMARK 500 O HOH A 635 O HOH B 617 2455 2.06 REMARK 500 O HOH A 460 O HOH A 527 4455 2.09 REMARK 500 OE1 GLU B 227 O HOH A 404 3444 2.12 REMARK 500 OD2 ASP B 223 O HOH A 405 3444 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 PHE A 70 -41.15 -132.79 REMARK 500 ASP A 90 141.43 76.69 REMARK 500 PHE B 70 -32.52 -130.65 REMARK 500 ASP B 90 138.62 76.11 REMARK 500 HIS B 120 171.94 177.54 REMARK 500 ASN B 142 131.33 -39.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 686 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 687 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 688 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 689 DISTANCE = 7.52 ANGSTROMS REMARK 525 HOH B 667 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH B 668 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH B 669 DISTANCE = 6.36 ANGSTROMS 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 122 ND1 103.1 REMARK 620 3 HIS A 189 NE2 97.1 121.9 REMARK 620 4 OL6 A 303 O4 174.1 82.8 79.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD2 REMARK 620 2 CYS A 208 SG 100.2 REMARK 620 3 HIS A 250 NE2 89.9 111.0 REMARK 620 4 OL6 A 303 N 98.1 134.4 110.4 REMARK 620 5 OL6 A 303 O 163.7 95.8 87.2 68.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 120 NE2 REMARK 620 2 HIS B 122 ND1 96.9 REMARK 620 3 HIS B 189 NE2 104.4 120.7 REMARK 620 4 OL6 B 303 O5 176.8 85.5 76.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 124 OD2 REMARK 620 2 CYS B 208 SG 98.4 REMARK 620 3 HIS B 250 NE2 93.9 116.5 REMARK 620 4 OL6 B 303 N 98.5 133.3 105.4 REMARK 620 5 OL6 B 303 O 161.8 99.3 82.2 65.8 REMARK 620 N 1 2 3 4 DBREF 8I8F A 1 270 UNP E9NWK5 E9NWK5_KLEPN 1 270 DBREF 8I8F B 1 270 UNP E9NWK5 E9NWK5_KLEPN 1 270 SEQRES 1 A 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 A 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 A 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 A 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 A 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 A 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 A 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 A 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 A 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 A 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 A 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 A 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 A 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 A 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 A 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 A 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 A 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 A 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 A 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 A 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 A 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 270 MET GLU LEU PRO ASN ILE MET HIS PRO VAL ALA LYS LEU SEQRES 2 B 270 SER THR ALA LEU ALA ALA ALA LEU MET LEU SER GLY CYS SEQRES 3 B 270 MET PRO GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET SEQRES 4 B 270 GLU THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG SEQRES 5 B 270 GLN LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU SEQRES 6 B 270 ASP MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU SEQRES 7 B 270 ILE VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR SEQRES 8 B 270 ALA TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP SEQRES 9 B 270 ILE LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL SEQRES 10 B 270 VAL THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP SEQRES 11 B 270 ALA LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA SEQRES 12 B 270 LEU SER ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA SEQRES 13 B 270 ALA GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL SEQRES 14 B 270 GLU PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL SEQRES 15 B 270 PHE TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR SEQRES 16 B 270 VAL GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS SEQRES 17 B 270 LEU ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU SEQRES 18 B 270 GLY ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG SEQRES 19 B 270 ALA PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL SEQRES 20 B 270 MET SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR SEQRES 21 B 270 HIS THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET OL6 A 303 49 HET ZN B 301 1 HET ZN B 302 1 HET OL6 B 303 49 HETNAM ZN ZINC ION HETNAM OL6 (2R,4S)-5,5-DIMETHYL-2-[(1R)-1-(2-NAPHTHALEN-1- HETNAM 2 OL6 YLOXYETHANOYLAMINO)-2-OXIDANYL-2-OXIDANYLIDENE-ETHYL]- HETNAM 3 OL6 1,3-THIAZOLIDINE-4-CARBOXYLIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 OL6 2(C20 H22 N2 O6 S) FORMUL 9 HOH *558(H2 O) HELIX 1 AA1 THR A 94 ILE A 109 1 16 HELIX 2 AA2 HIS A 122 GLY A 127 1 6 HELIX 3 AA3 GLY A 128 ALA A 135 1 8 HELIX 4 AA4 ALA A 143 ALA A 149 1 7 HELIX 5 AA5 PRO A 150 GLY A 153 5 4 HELIX 6 AA6 GLU A 170 ALA A 174 5 5 HELIX 7 AA7 GLY A 207 ILE A 210 5 4 HELIX 8 AA8 HIS A 228 PHE A 240 1 13 HELIX 9 AA9 ARG A 256 LYS A 268 1 13 HELIX 10 AB1 THR B 94 ILE B 109 1 16 HELIX 11 AB2 HIS B 122 GLY B 127 1 6 HELIX 12 AB3 GLY B 128 ALA B 135 1 8 HELIX 13 AB4 ALA B 143 ALA B 149 1 7 HELIX 14 AB5 PRO B 150 GLY B 153 5 4 HELIX 15 AB6 GLU B 170 ALA B 174 5 5 HELIX 16 AB7 CYS B 208 ILE B 210 5 3 HELIX 17 AB8 HIS B 228 PHE B 240 1 13 HELIX 18 AB9 ARG B 256 LYS B 268 1 13 SHEET 1 AA1 8 ASP A 43 PHE A 46 0 SHEET 2 AA1 8 LEU A 49 ALA A 55 -1 O PHE A 51 N GLN A 44 SHEET 3 AA1 8 VAL A 58 MET A 67 -1 O GLN A 60 N ARG A 52 SHEET 4 AA1 8 GLY A 71 ASP A 82 -1 O GLY A 71 N MET A 67 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O LEU A 87 N VAL A 80 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O VAL A 117 N VAL A 88 SHEET 7 AA1 8 ALA A 138 ASN A 142 1 O TYR A 140 N ALA A 116 SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141 SHEET 1 AA2 4 LEU A 180 PHE A 183 0 SHEET 2 AA2 4 THR A 195 ILE A 198 -1 O THR A 195 N PHE A 183 SHEET 3 AA2 4 ILE A 203 PHE A 205 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 VAL A 247 1 O VAL A 247 N ALA A 204 SHEET 1 AA3 8 ASP B 43 PHE B 46 0 SHEET 2 AA3 8 LEU B 49 ALA B 55 -1 O PHE B 51 N GLN B 44 SHEET 3 AA3 8 VAL B 58 MET B 67 -1 O GLN B 60 N ARG B 52 SHEET 4 AA3 8 GLY B 71 ASP B 82 -1 O ILE B 79 N TRP B 59 SHEET 5 AA3 8 ARG B 85 VAL B 89 -1 O LEU B 87 N VAL B 80 SHEET 6 AA3 8 VAL B 113 VAL B 117 1 O ALA B 114 N VAL B 86 SHEET 7 AA3 8 ALA B 138 ASN B 142 1 O TYR B 140 N ALA B 116 SHEET 8 AA3 8 HIS B 159 LEU B 161 1 O LEU B 161 N ALA B 141 SHEET 1 AA4 4 LEU B 180 PHE B 183 0 SHEET 2 AA4 4 THR B 195 ILE B 198 -1 O THR B 195 N PHE B 183 SHEET 3 AA4 4 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196 SHEET 4 AA4 4 MET B 245 MET B 248 1 O VAL B 247 N GLY B 206 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.22 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.15 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.13 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.20 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.33 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.19 LINK ZN ZN A 301 O4 OL6 A 303 1555 1555 2.63 LINK ZN ZN A 302 N OL6 A 303 1555 1555 2.33 LINK ZN ZN A 302 O OL6 A 303 1555 1555 2.28 LINK NE2 HIS B 120 ZN ZN B 301 1555 1555 2.21 LINK ND1 HIS B 122 ZN ZN B 301 1555 1555 2.14 LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.15 LINK NE2 HIS B 189 ZN ZN B 301 1555 1555 2.19 LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.34 LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 2.17 LINK ZN ZN B 301 O5 OL6 B 303 1555 1555 2.70 LINK ZN ZN B 302 N OL6 B 303 1555 1555 2.25 LINK ZN ZN B 302 O OL6 B 303 1555 1555 2.44 CRYST1 39.114 78.847 133.534 90.00 90.00 90.00 P 21 21 21 8 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 0.025566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007489 0.00000