HEADER HYDROLASE/ANTIBIOTIC 16-APR-19 6OL8 TITLE CRYSTAL STRUCTURE OF NDM-12 METALLO-BETA-LACTAMASE IN COMPLEX WITH TITLE 2 HYDROLYZED AMPICILLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE NDM-12; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BLANDM-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLO-BETA-LACTAMASE, NDM, HYDROLASE, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.E.RACZYNSKA,B.IMIOLCZYK,M.JASKOLSKI REVDAT 4 11-OCT-23 6OL8 1 LINK REVDAT 3 20-MAY-20 6OL8 1 JRNL REVDAT 2 13-MAY-20 6OL8 1 JRNL REVDAT 1 22-APR-20 6OL8 0 JRNL AUTH J.E.RACZYNSKA,B.IMIOLCZYK,M.KOMOROWSKA,J.SLIWIAK, JRNL AUTH 2 J.CZYRKO-HORCZAK,K.BRZEZINSKI,M.JASKOLSKI JRNL TITL FLEXIBLE LOOPS OF NEW DELHI METALLO-BETA-LACTAMASE MODULATE JRNL TITL 2 ITS ACTIVITY TOWARDS DIFFERENT SUBSTRATES. JRNL REF INT.J.BIOL.MACROMOL. V. 158 104 2020 JRNL REFN ISSN 0141-8130 JRNL PMID 32353499 JRNL DOI 10.1016/J.IJBIOMAC.2020.04.219 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 21606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1160 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3566 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.57000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : 1.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.299 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.350 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3763 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3366 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5130 ; 1.614 ; 1.640 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7789 ; 1.398 ; 1.590 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 487 ; 7.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;31.176 ;23.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;14.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.608 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4402 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 769 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1939 ; 2.403 ; 1.957 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1938 ; 2.401 ; 1.956 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2426 ; 3.340 ; 2.930 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2427 ; 3.341 ; 2.932 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1824 ; 3.555 ; 2.302 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1825 ; 3.554 ; 2.303 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2704 ; 4.867 ; 3.321 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 16981 ; 6.573 ;38.086 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 16861 ; 6.571 ;37.914 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 31 270 B 31 270 7870 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 31 A 52 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1740 13.2500 44.6370 REMARK 3 T TENSOR REMARK 3 T11: 0.1815 T22: 0.4349 REMARK 3 T33: 0.1415 T12: 0.0364 REMARK 3 T13: 0.0388 T23: -0.0719 REMARK 3 L TENSOR REMARK 3 L11: 0.5626 L22: 3.5438 REMARK 3 L33: 7.1315 L12: 0.6855 REMARK 3 L13: -0.5670 L23: -2.0681 REMARK 3 S TENSOR REMARK 3 S11: -0.0719 S12: 0.1266 S13: -0.2372 REMARK 3 S21: -0.2030 S22: -0.0938 S23: -0.5653 REMARK 3 S31: 0.7538 S32: 0.4771 S33: 0.1657 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 53 A 270 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4280 29.1790 51.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.2523 REMARK 3 T33: 0.0055 T12: -0.0098 REMARK 3 T13: 0.0073 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.9157 L22: 0.8786 REMARK 3 L33: 0.8509 L12: 0.0351 REMARK 3 L13: -0.0646 L23: -0.3349 REMARK 3 S TENSOR REMARK 3 S11: -0.0072 S12: 0.0368 S13: -0.0334 REMARK 3 S21: -0.0798 S22: -0.0154 S23: -0.0625 REMARK 3 S31: 0.0398 S32: 0.0182 S33: 0.0225 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 31 B 114 REMARK 3 ORIGIN FOR THE GROUP (A): 29.6570 42.5320 81.5830 REMARK 3 T TENSOR REMARK 3 T11: 0.1780 T22: 0.1888 REMARK 3 T33: 0.0476 T12: 0.0218 REMARK 3 T13: -0.0460 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 2.5799 L22: 1.1786 REMARK 3 L33: 3.0215 L12: -0.0334 REMARK 3 L13: 1.1345 L23: 0.2772 REMARK 3 S TENSOR REMARK 3 S11: 0.2329 S12: -0.0439 S13: -0.3159 REMARK 3 S21: 0.1867 S22: -0.0712 S23: 0.0576 REMARK 3 S31: 0.3672 S32: 0.0970 S33: -0.1617 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 115 B 270 REMARK 3 ORIGIN FOR THE GROUP (A): 27.6120 59.5460 82.8050 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.2545 REMARK 3 T33: 0.0053 T12: 0.0076 REMARK 3 T13: -0.0162 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.5570 L22: 1.3080 REMARK 3 L33: 1.0320 L12: -0.0584 REMARK 3 L13: 0.2518 L23: 0.2488 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: 0.0413 S13: -0.0394 REMARK 3 S21: 0.0395 S22: -0.0406 S23: 0.0301 REMARK 3 S31: 0.0058 S32: -0.0591 S33: 0.0389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS WERE ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6OL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918400 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 66.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 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 REMARK 200 STARTING MODEL: 3Q6X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M KBR, 30% PEG 2000 MME, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 19.23450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.45300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.22450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.45300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.23450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.22450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 GLY A 28 REMARK 465 GLY A 29 REMARK 465 GLU A 30 REMARK 465 GLY B 28 REMARK 465 GLY B 29 REMARK 465 GLU B 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 ILE A 31 CG1 CG2 CD1 REMARK 470 ASP A 66 CG OD1 OD2 REMARK 470 ILE B 31 CG1 CG2 CD1 REMARK 470 ARG B 45 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 48 CG OD1 OD2 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 90 142.87 74.10 REMARK 500 HIS A 120 168.10 179.95 REMARK 500 ASN A 142 125.58 -39.97 REMARK 500 ASP B 90 141.41 76.40 REMARK 500 HIS B 120 165.74 171.47 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 B 507 DISTANCE = 5.83 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 103.5 REMARK 620 3 HIS A 189 NE2 94.0 125.9 REMARK 620 4 ZZ7 A 308 OXT 169.0 86.9 82.4 REMARK 620 5 HOH A 411 O 90.1 124.4 105.9 80.9 REMARK 620 N 1 2 3 4 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 93.4 REMARK 620 3 HIS A 250 NE2 88.3 108.5 REMARK 620 4 ZZ7 A 308 O1 170.1 95.0 93.9 REMARK 620 5 ZZ7 A 308 N3 93.4 132.1 119.0 77.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 307 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 48.6 REMARK 620 3 ASP A 223 OD1 158.3 141.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 227 OE2 REMARK 620 2 GLU B 152 OE1 73.7 REMARK 620 3 GLU B 152 OE2 74.0 2.5 REMARK 620 4 ASP B 223 OD1 77.7 4.2 3.8 REMARK 620 5 ASP B 223 OD2 77.2 3.7 3.5 0.6 REMARK 620 6 HOH B 450 O 74.2 0.8 3.1 4.0 3.4 REMARK 620 N 1 2 3 4 5 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 103.4 REMARK 620 3 HIS B 189 NE2 94.4 120.8 REMARK 620 4 ZZ7 B 305 OXT 169.2 85.6 85.8 REMARK 620 5 HOH B 407 O 92.4 124.5 110.3 77.5 REMARK 620 N 1 2 3 4 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 90.3 REMARK 620 3 HIS B 250 NE2 89.8 107.1 REMARK 620 4 ZZ7 B 305 O1 174.2 94.9 86.2 REMARK 620 5 ZZ7 B 305 N3 97.7 134.4 117.7 80.5 REMARK 620 6 HOH B 407 O 73.0 71.7 162.6 111.1 68.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZZ7 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZZ7 B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6OGO RELATED DB: PDB DBREF1 6OL8 A 29 270 UNP A0A024FRL9_ECOLX DBREF2 6OL8 A A0A024FRL9 29 270 DBREF1 6OL8 B 29 270 UNP A0A024FRL9_ECOLX DBREF2 6OL8 B A0A024FRL9 29 270 SEQADV 6OL8 GLY A 28 UNP A0A024FRL EXPRESSION TAG SEQADV 6OL8 GLY B 28 UNP A0A024FRL EXPRESSION TAG SEQRES 1 A 243 GLY GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 A 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 A 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 A 243 MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 A 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 A 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 A 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 A 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 A 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 A 243 SER ASN GLN LEU ALA PRO GLN GLU GLY LEU VAL ALA ALA SEQRES 11 A 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 A 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 A 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 A 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 A 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU ASP SEQRES 16 A 243 ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 A 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 A 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 A 243 THR ALA ARG MET ALA ASP LYS LEU ARG SEQRES 1 B 243 GLY GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU SEQRES 2 B 243 THR GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN SEQRES 3 B 243 LEU ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP SEQRES 4 B 243 MET PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE SEQRES 5 B 243 VAL ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA SEQRES 6 B 243 TRP THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE SEQRES 7 B 243 LYS GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL SEQRES 8 B 243 THR HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA SEQRES 9 B 243 LEU HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SEQRES 10 B 243 SER ASN GLN LEU ALA PRO GLN GLU GLY LEU VAL ALA ALA SEQRES 11 B 243 GLN HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU SEQRES 12 B 243 PRO ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE SEQRES 13 B 243 TYR PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL SEQRES 14 B 243 GLY ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU SEQRES 15 B 243 ILE LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU ASP SEQRES 16 B 243 ASP ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA SEQRES 17 B 243 PHE GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SEQRES 18 B 243 SER HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS SEQRES 19 B 243 THR ALA ARG MET ALA ASP LYS LEU ARG HET ZN A 301 1 HET ZN A 302 1 HET CL A 303 1 HET CL A 304 1 HET CL A 305 1 HET CL A 306 1 HET NA A 307 1 HET ZZ7 A 308 25 HET ZN B 301 1 HET ZN B 302 1 HET CL B 303 1 HET NA B 304 1 HET ZZ7 B 305 25 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM ZZ7 (2R,4S)-2-[(R)-{[(2R)-2-AMINO-2- HETNAM 2 ZZ7 PHENYLACETYL]AMINO}(CARBOXY)METHYL]-5,5-DIMETHYL-1,3- HETNAM 3 ZZ7 THIAZOLIDINE-4-CARBOXYLIC ACID HETSYN ZZ7 AMPICILLIN (OPEN FORM) FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CL 5(CL 1-) FORMUL 9 NA 2(NA 1+) FORMUL 10 ZZ7 2(C16 H21 N3 O5 S) FORMUL 16 HOH *231(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 HIS A 228 PHE A 240 1 13 HELIX 8 AA8 ARG A 256 LYS A 268 1 13 HELIX 9 AA9 THR B 94 ILE B 109 1 16 HELIX 10 AB1 HIS B 122 GLY B 127 1 6 HELIX 11 AB2 GLY B 128 ALA B 135 1 8 HELIX 12 AB3 ALA B 143 ALA B 149 1 7 HELIX 13 AB4 PRO B 150 GLY B 153 5 4 HELIX 14 AB5 GLU B 170 ALA B 174 5 5 HELIX 15 AB6 HIS B 228 PHE B 240 1 13 HELIX 16 AB7 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 ILE A 79 N TRP A 59 SHEET 5 AA1 8 ARG A 85 VAL A 89 -1 O VAL A 89 N LEU A 78 SHEET 6 AA1 8 VAL A 113 VAL A 117 1 O ALA A 114 N VAL A 86 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 GLY A 207 -1 O PHE A 205 N VAL A 196 SHEET 4 AA2 4 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206 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 VAL B 89 N LEU B 78 SHEET 6 AA3 8 VAL B 113 VAL B 117 1 O VAL B 117 N VAL B 88 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 PHE B 205 -1 O ILE B 203 N ILE B 198 SHEET 4 AA4 4 MET B 245 VAL B 247 1 O VAL B 247 N ALA B 204 LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.12 LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 1.91 LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.00 LINK OE1 GLU A 152 NA NA A 307 1555 1555 2.87 LINK OE2 GLU A 152 NA NA A 307 1555 1555 2.32 LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 1.96 LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.42 LINK OD1 ASP A 223 NA NA A 307 1555 1555 2.95 LINK OE2 GLU A 227 NA NA B 304 1555 4466 2.50 LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 1.90 LINK ZN ZN A 301 OXT ZZ7 A 308 1555 1555 2.25 LINK ZN ZN A 301 O HOH A 411 1555 1555 1.84 LINK ZN ZN A 302 O1 ZZ7 A 308 1555 1555 2.09 LINK ZN ZN A 302 N3 ZZ7 A 308 1555 1555 2.16 LINK NE2 HIS B 120 ZN ZN B 301 1555 1555 2.21 LINK ND1 HIS B 122 ZN ZN B 301 1555 1555 1.86 LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.02 LINK OE1 GLU B 152 NA NA B 304 1555 1555 2.55 LINK OE2 GLU B 152 NA NA B 304 1555 1555 2.30 LINK NE2 HIS B 189 ZN ZN B 301 1555 1555 1.85 LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.34 LINK OD1 ASP B 223 NA NA B 304 1555 1555 2.94 LINK OD2 ASP B 223 NA NA B 304 1555 1555 1.92 LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 1.91 LINK ZN ZN B 301 OXT ZZ7 B 305 1555 1555 2.23 LINK ZN ZN B 301 O HOH B 407 1555 1555 1.85 LINK ZN ZN B 302 O1 ZZ7 B 305 1555 1555 2.08 LINK ZN ZN B 302 N3 ZZ7 B 305 1555 1555 2.15 LINK ZN ZN B 302 O HOH B 407 1555 1555 2.68 LINK NA NA B 304 O HOH B 450 1555 1555 1.91 SITE 1 AC1 5 HIS A 120 HIS A 122 HIS A 189 ZZ7 A 308 SITE 2 AC1 5 HOH A 411 SITE 1 AC2 5 ASP A 124 CYS A 208 HIS A 250 ZZ7 A 308 SITE 2 AC2 5 HOH A 411 SITE 1 AC3 2 ALA A 55 PRO A 56 SITE 1 AC4 4 PHE A 240 PRO A 241 LYS A 242 ALA A 243 SITE 1 AC5 1 ASN A 166 SITE 1 AC6 2 GLU A 152 ASP A 223 SITE 1 AC7 19 LEU A 65 MET A 67 TRP A 93 HIS A 122 SITE 2 AC7 19 GLN A 123 ASP A 124 HIS A 189 CYS A 208 SITE 3 AC7 19 LYS A 211 GLY A 219 ASN A 220 HIS A 250 SITE 4 AC7 19 ZN A 301 ZN A 302 HOH A 411 HOH A 469 SITE 5 AC7 19 HOH A 480 THR B 34 GLY B 69 SITE 1 AC8 5 HIS B 120 HIS B 122 HIS B 189 ZZ7 B 305 SITE 2 AC8 5 HOH B 407 SITE 1 AC9 5 ASP B 124 CYS B 208 HIS B 250 ZZ7 B 305 SITE 2 AC9 5 HOH B 407 SITE 1 AD1 3 ALA B 55 ASN B 57 HOH B 500 SITE 1 AD2 4 GLU A 227 GLU B 152 ASP B 223 HOH B 450 SITE 1 AD3 20 THR A 34 PRO A 68 GLY A 69 PHE A 70 SITE 2 AD3 20 MET B 67 TRP B 93 HIS B 122 GLN B 123 SITE 3 AD3 20 ASP B 124 HIS B 189 CYS B 208 LYS B 211 SITE 4 AD3 20 GLY B 219 ASN B 220 HIS B 250 ZN B 301 SITE 5 AD3 20 ZN B 302 HOH B 407 HOH B 419 HOH B 465 CRYST1 38.469 76.449 130.906 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 0.025995 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007639 0.00000