HEADER ANTIMICROBIAL PROTEIN 26-FEB-20 6Y6J TITLE VIM-2 IN COMPLEX WITH BIAPENEM IMINE AND ENAMINE HYDROLYSIS PRODUCTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE VIM-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: BLAVIM-2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: LEMO21 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPINF KEYWDS METALLO BETA LACTAMASES, VIM2, BIAPENEM, ENZYME PRODUCT COMPLEX, KEYWDS 2 ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.LUCIC,C.J.SCHOFIELD,J.BREM,M.A.MCDONOUGH REVDAT 2 24-JAN-24 6Y6J 1 REMARK REVDAT 1 31-MAR-21 6Y6J 0 JRNL AUTH A.LUCIC,B.G.SAWARD,J.BREM,M.A.MCDONOUGH,K.CALVOPINA, JRNL AUTH 2 C.J.SCHOFIELD JRNL TITL STRUCTURE OF METALLO-BETA-LACTAMASE VIM-2 IN COMPLEX WITH JRNL TITL 2 THE IMINE AND ENAMINE FORM OF HYDROLYSED BIAPENEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 30179 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1406 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 27.6100 - 3.2300 1.00 3042 150 0.1347 0.1711 REMARK 3 2 3.2300 - 2.5600 1.00 2926 141 0.1332 0.1563 REMARK 3 3 2.5600 - 2.2400 1.00 2884 139 0.1243 0.1416 REMARK 3 4 2.2400 - 2.0400 1.00 2889 141 0.1232 0.1478 REMARK 3 5 2.0400 - 1.8900 1.00 2865 144 0.1193 0.1570 REMARK 3 6 1.8900 - 1.7800 1.00 2865 132 0.1242 0.1484 REMARK 3 7 1.7800 - 1.6900 0.99 2820 142 0.1252 0.1395 REMARK 3 8 1.6900 - 1.6200 0.99 2835 143 0.1223 0.1571 REMARK 3 9 1.6200 - 1.5500 0.99 2830 139 0.1302 0.1607 REMARK 3 10 1.5500 - 1.5000 0.99 2816 135 0.1391 0.1833 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.08 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 : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.6147 -3.7744 -2.3801 REMARK 3 T TENSOR REMARK 3 T11: 0.2616 T22: 0.1241 REMARK 3 T33: 0.1586 T12: 0.0121 REMARK 3 T13: -0.0105 T23: -0.0557 REMARK 3 L TENSOR REMARK 3 L11: 6.0843 L22: 0.7452 REMARK 3 L33: 5.6037 L12: -0.6256 REMARK 3 L13: 2.1830 L23: 0.3640 REMARK 3 S TENSOR REMARK 3 S11: -0.1804 S12: -0.3803 S13: 0.5789 REMARK 3 S21: 0.2893 S22: 0.1126 S23: -0.1885 REMARK 3 S31: -0.4810 S32: -0.1791 S33: 0.1480 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 45 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4824 -7.7692 -6.7821 REMARK 3 T TENSOR REMARK 3 T11: 0.1882 T22: 0.0761 REMARK 3 T33: 0.0622 T12: 0.0085 REMARK 3 T13: -0.0028 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 8.2947 L22: 2.2243 REMARK 3 L33: 3.5862 L12: 0.0763 REMARK 3 L13: -0.5289 L23: 1.2737 REMARK 3 S TENSOR REMARK 3 S11: -0.0047 S12: -0.2616 S13: 0.1564 REMARK 3 S21: 0.1138 S22: 0.0946 S23: -0.0762 REMARK 3 S31: -0.0972 S32: 0.1966 S33: -0.0963 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5366 -10.2382 -12.7464 REMARK 3 T TENSOR REMARK 3 T11: 0.1498 T22: 0.0393 REMARK 3 T33: 0.0577 T12: -0.0079 REMARK 3 T13: 0.0056 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 8.8928 L22: 1.1325 REMARK 3 L33: 3.3705 L12: 0.2564 REMARK 3 L13: -3.5070 L23: 0.1818 REMARK 3 S TENSOR REMARK 3 S11: 0.0803 S12: -0.0206 S13: 0.1952 REMARK 3 S21: -0.0311 S22: 0.0388 S23: -0.0312 REMARK 3 S31: -0.0773 S32: 0.1645 S33: -0.1198 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 89 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.0901 -1.4472 -15.3027 REMARK 3 T TENSOR REMARK 3 T11: 0.2291 T22: 0.0606 REMARK 3 T33: 0.1312 T12: 0.0045 REMARK 3 T13: 0.0388 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 7.5808 L22: 8.0273 REMARK 3 L33: 1.2974 L12: 3.9718 REMARK 3 L13: -0.0155 L23: -0.5373 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: -0.1607 S13: 0.4858 REMARK 3 S21: 0.1130 S22: 0.0344 S23: -0.1810 REMARK 3 S31: -0.3468 S32: 0.0881 S33: -0.0448 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 103 THROUGH 199 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0065 -19.9120 -17.3303 REMARK 3 T TENSOR REMARK 3 T11: 0.1304 T22: 0.0620 REMARK 3 T33: 0.0560 T12: 0.0102 REMARK 3 T13: -0.0001 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 1.7809 L22: 1.4132 REMARK 3 L33: 1.5779 L12: 0.1066 REMARK 3 L13: -0.2296 L23: -0.1986 REMARK 3 S TENSOR REMARK 3 S11: 0.0330 S12: 0.0441 S13: -0.0874 REMARK 3 S21: -0.0828 S22: 0.0104 S23: -0.0104 REMARK 3 S31: 0.0358 S32: 0.0836 S33: -0.0402 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 200 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.2658 -23.1986 -0.6727 REMARK 3 T TENSOR REMARK 3 T11: 0.2372 T22: 0.1598 REMARK 3 T33: 0.1299 T12: -0.0106 REMARK 3 T13: -0.0023 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.8141 L22: 7.6558 REMARK 3 L33: 8.9686 L12: 2.1666 REMARK 3 L13: 2.3964 L23: 8.2789 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: -0.3091 S13: -0.0475 REMARK 3 S21: 0.1564 S22: -0.3877 S23: 0.5739 REMARK 3 S31: 0.0372 S32: -0.6581 S33: 0.4291 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.8661 -30.9865 -3.5796 REMARK 3 T TENSOR REMARK 3 T11: 0.2587 T22: 0.1660 REMARK 3 T33: 0.1193 T12: 0.0936 REMARK 3 T13: -0.0210 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 7.7859 L22: 3.9809 REMARK 3 L33: 1.9586 L12: 2.6052 REMARK 3 L13: 1.7935 L23: 0.1164 REMARK 3 S TENSOR REMARK 3 S11: 0.2027 S12: 0.0637 S13: -0.6495 REMARK 3 S21: 0.2115 S22: -0.0869 S23: -0.2588 REMARK 3 S31: 0.4732 S32: 0.4179 S33: -0.1093 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 230 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7913 -16.9072 -1.8608 REMARK 3 T TENSOR REMARK 3 T11: 0.1801 T22: 0.2768 REMARK 3 T33: 0.0807 T12: -0.0411 REMARK 3 T13: -0.0446 T23: 0.0222 REMARK 3 L TENSOR REMARK 3 L11: 4.7450 L22: 3.0045 REMARK 3 L33: 0.5707 L12: -2.2528 REMARK 3 L13: -0.6281 L23: -0.1715 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: -0.1695 S13: 0.2126 REMARK 3 S21: 0.3471 S22: -0.0426 S23: -0.3323 REMARK 3 S31: -0.2416 S32: 0.6286 S33: 0.0650 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8094 -27.6307 4.1954 REMARK 3 T TENSOR REMARK 3 T11: 0.2334 T22: 0.1062 REMARK 3 T33: 0.0837 T12: 0.0290 REMARK 3 T13: -0.0213 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 8.8161 L22: 7.2935 REMARK 3 L33: 6.9050 L12: 3.6292 REMARK 3 L13: 0.7512 L23: 0.0804 REMARK 3 S TENSOR REMARK 3 S11: -0.0294 S12: -0.3307 S13: -0.4415 REMARK 3 S21: 0.0982 S22: 0.0010 S23: 0.0583 REMARK 3 S31: 0.3412 S32: -0.0759 S33: 0.0149 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 6Y6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292106640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 27.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.35 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: 4BZ3 REMARK 200 REMARK 200 REMARK: 100 X 20 X 10 MICROMETER CRYSTAL, RHOMBOID SHAPE CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% W/V PEG 8000, 0.2M MAGNESIUM REMARK 280 CHLORIDE, 0.1M TRIS PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.16200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.01000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.17700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.16200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.01000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.17700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.16200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.01000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.17700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.16200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.01000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.17700 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: 450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL 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 906 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 937 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 993 LIES ON A SPECIAL POSITION. 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 LYS A 90 CD CE NZ REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 GLN A 228 CG CD OE1 NE2 REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 SER A 263 CA C O CB OG 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 A 84 147.61 72.35 REMARK 500 TRP A 87 70.45 69.74 REMARK 500 ALA A 178 -106.69 -151.66 REMARK 500 ARG A 262 107.74 -59.09 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 995 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 6.19 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 703 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 114 NE2 REMARK 620 2 HIS A 116 ND1 99.8 REMARK 620 3 HIS A 179 NE2 101.2 116.8 REMARK 620 4 OEN A 701 O2 115.5 100.9 121.2 REMARK 620 5 OEQ A 702 O2 117.4 103.9 117.0 4.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 704 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 118 OD2 REMARK 620 2 CYS A 198 SG 101.2 REMARK 620 3 HIS A 240 NE2 87.4 106.5 REMARK 620 4 OEN A 701 N3 91.1 150.3 101.0 REMARK 620 5 OEN A 701 O4 167.4 91.4 88.9 77.8 REMARK 620 6 OEQ A 702 O 162.1 96.8 87.6 73.0 5.4 REMARK 620 7 OEQ A 702 N3 87.0 157.6 94.6 7.5 81.3 76.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 705 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 153 NE2 REMARK 620 2 HIS A 251 ND1 46.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OEN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OEQ A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 708 DBREF 6Y6J A 32 263 UNP D1MEN9 D1MEN9_PSEAI 32 263 SEQRES 1 A 232 GLU TYR PRO THR VAL SER GLU ILE PRO VAL GLY GLU VAL SEQRES 2 A 232 ARG LEU TYR GLN ILE ALA ASP GLY VAL TRP SER HIS ILE SEQRES 3 A 232 ALA THR GLN SER PHE ASP GLY ALA VAL TYR PRO SER ASN SEQRES 4 A 232 GLY LEU ILE VAL ARG ASP GLY ASP GLU LEU LEU LEU ILE SEQRES 5 A 232 ASP THR ALA TRP GLY ALA LYS ASN THR ALA ALA LEU LEU SEQRES 6 A 232 ALA GLU ILE GLU LYS GLN ILE GLY LEU PRO VAL THR ARG SEQRES 7 A 232 ALA VAL SER THR HIS PHE HIS ASP ASP ARG VAL GLY GLY SEQRES 8 A 232 VAL ASP VAL LEU ARG ALA ALA GLY VAL ALA THR TYR ALA SEQRES 9 A 232 SER PRO SER THR ARG ARG LEU ALA GLU VAL GLU GLY ASN SEQRES 10 A 232 GLU ILE PRO THR HIS SER LEU GLU GLY LEU SER SER SER SEQRES 11 A 232 GLY ASP ALA VAL ARG PHE GLY PRO VAL GLU LEU PHE TYR SEQRES 12 A 232 PRO GLY ALA ALA HIS SER THR ASP ASN LEU VAL VAL TYR SEQRES 13 A 232 VAL PRO SER ALA SER VAL LEU TYR GLY GLY CYS ALA ILE SEQRES 14 A 232 TYR GLU LEU SER ARG THR SER ALA GLY ASN VAL ALA ASP SEQRES 15 A 232 ALA ASP LEU ALA GLU TRP PRO THR SER ILE GLU ARG ILE SEQRES 16 A 232 GLN GLN HIS TYR PRO GLU ALA GLN PHE VAL ILE PRO GLY SEQRES 17 A 232 HIS GLY LEU PRO GLY GLY LEU ASP LEU LEU LYS HIS THR SEQRES 18 A 232 THR ASN VAL VAL LYS ALA HIS THR ASN ARG SER HET OEN A 701 25 HET OEQ A 702 25 HET ZN A 703 1 HET ZN A 704 1 HET ZN A 705 1 HET CL A 706 1 HET CL A 707 1 HET CL A 708 1 HETNAM OEN BIAPENEM IMINE HYDROLYSIS PRODUCT HETNAM OEQ BIAPENEM ENAMINE HYDROLYSIS PRODUCT HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN OEQ (2~{S},3~{R})-2-[(2~{S},3~{R})-1,3-BIS(OXIDANYL)-1- HETSYN 2 OEQ OXIDANYLIDENE-BUTAN-2-YL]-4-[[(6~{R})-6,7-DIHYDRO- HETSYN 3 OEQ 5~{H}-PYRAZOLO[1,2 -A][1,2,4]TRIAZOL-4-IUM-6- HETSYN 4 OEQ YL]SULFANYL]-3-METHYL-2,3-DIHYDRO-1~{H}-PYRROLE-5- HETSYN 5 OEQ CARBOXYLIC ACID FORMUL 2 OEN C15 H21 N4 O5 S 1+ FORMUL 3 OEQ C15 H21 N4 O5 S 1+ FORMUL 4 ZN 3(ZN 2+) FORMUL 7 CL 3(CL 1-) FORMUL 10 HOH *196(H2 O) HELIX 1 AA1 THR A 35 ILE A 39 5 5 HELIX 2 AA2 GLY A 88 ILE A 103 1 16 HELIX 3 AA3 HIS A 116 GLY A 121 1 6 HELIX 4 AA4 GLY A 122 ALA A 129 1 8 HELIX 5 AA5 SER A 136 GLY A 147 1 12 HELIX 6 AA6 CYS A 198 ILE A 200 5 3 HELIX 7 AA7 GLU A 218 TYR A 230 1 13 HELIX 8 AA8 LEU A 246 ARG A 262 1 17 SHEET 1 AA1 7 ARG A 45 ALA A 50 0 SHEET 2 AA1 7 VAL A 53 PHE A 62 -1 O ILE A 57 N ARG A 45 SHEET 3 AA1 7 ALA A 65 ASP A 76 -1 O ILE A 73 N TRP A 54 SHEET 4 AA1 7 GLU A 79 ILE A 83 -1 O GLU A 79 N ASP A 76 SHEET 5 AA1 7 VAL A 107 VAL A 111 1 O ARG A 109 N LEU A 82 SHEET 6 AA1 7 ALA A 132 ALA A 135 1 O ALA A 132 N THR A 108 SHEET 7 AA1 7 HIS A 153 SER A 154 1 O HIS A 153 N THR A 133 SHEET 1 AA2 5 ASP A 163 PHE A 167 0 SHEET 2 AA2 5 VAL A 170 TYR A 174 -1 O LEU A 172 N VAL A 165 SHEET 3 AA2 5 VAL A 185 VAL A 188 -1 O TYR A 187 N GLU A 171 SHEET 4 AA2 5 VAL A 193 GLY A 197 -1 O TYR A 195 N VAL A 186 SHEET 5 AA2 5 PHE A 235 PRO A 238 1 O PHE A 235 N LEU A 194 LINK NE2 HIS A 114 ZN ZN A 703 1555 1555 2.06 LINK ND1 HIS A 116 ZN ZN A 703 1555 1555 2.00 LINK OD2 ASP A 118 ZN ZN A 704 1555 1555 2.10 LINK NE2 HIS A 153 ZN ZN A 705 1555 1555 2.08 LINK NE2 HIS A 179 ZN ZN A 703 1555 1555 1.98 LINK SG CYS A 198 ZN ZN A 704 1555 1555 2.32 LINK NE2 HIS A 240 ZN ZN A 704 1555 1555 2.06 LINK ND1 HIS A 251 ZN ZN A 705 1555 6445 2.02 LINK O2 AOEN A 701 ZN ZN A 703 1555 1555 1.92 LINK N3 AOEN A 701 ZN ZN A 704 1555 1555 2.06 LINK O4 AOEN A 701 ZN ZN A 704 1555 1555 2.19 LINK O2 BOEQ A 702 ZN ZN A 703 1555 1555 2.01 LINK O BOEQ A 702 ZN ZN A 704 1555 1555 2.36 LINK N3 BOEQ A 702 ZN ZN A 704 1555 1555 2.17 SITE 1 AC1 19 PHE A 62 ASP A 63 TYR A 67 TRP A 87 SITE 2 AC1 19 HIS A 114 HIS A 116 ASP A 117 ASP A 118 SITE 3 AC1 19 HIS A 179 CYS A 198 ARG A 205 ASN A 210 SITE 4 AC1 19 HIS A 240 OEQ A 702 ZN A 703 ZN A 704 SITE 5 AC1 19 HOH A 841 HOH A 905 HOH A 944 SITE 1 AC2 20 PHE A 62 ASP A 63 TYR A 67 TRP A 87 SITE 2 AC2 20 HIS A 114 HIS A 116 ASP A 117 ASP A 118 SITE 3 AC2 20 HIS A 179 CYS A 198 ARG A 205 GLY A 209 SITE 4 AC2 20 ASN A 210 HIS A 240 OEN A 701 ZN A 703 SITE 5 AC2 20 ZN A 704 HOH A 831 HOH A 841 HOH A 905 SITE 1 AC3 5 HIS A 114 HIS A 116 HIS A 179 OEN A 701 SITE 2 AC3 5 OEQ A 702 SITE 1 AC4 5 ASP A 118 CYS A 198 HIS A 240 OEN A 701 SITE 2 AC4 5 OEQ A 702 SITE 1 AC5 4 HIS A 153 HIS A 251 CL A 706 CL A 707 SITE 1 AC6 4 HIS A 153 HIS A 251 ZN A 705 HOH A 819 SITE 1 AC7 5 ALA A 132 HIS A 153 HIS A 251 ASN A 254 SITE 2 AC7 5 ZN A 705 SITE 1 AC8 4 HIS A 116 ASP A 117 ASN A 148 HOH A 967 CRYST1 64.324 74.020 78.354 90.00 90.00 90.00 I 2 2 2 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 0.015546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013510 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012763 0.00000