HEADER HYDROLASE 23-NOV-15 5B15 TITLE CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE SMB-1 BOUND TO HYDROLYZED TITLE 2 DORIPENEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS; SOURCE 3 ORGANISM_TAXID: 615; SOURCE 4 GENE: SMB-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.WACHINO,Y.ARAKAWA REVDAT 4 23-OCT-24 5B15 1 REMARK REVDAT 3 08-NOV-23 5B15 1 REMARK LINK REVDAT 2 06-JUL-16 5B15 1 REMARK REVDAT 1 11-MAY-16 5B15 0 JRNL AUTH J.WACHINO,Y.ARAKAWA JRNL TITL CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE SMB-1 BOUND TO JRNL TITL 2 HYDROLYZED DORIPENEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 3 NUMBER OF REFLECTIONS : 37585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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) : 1.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2641 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.1600 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.1920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1921 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.39000 REMARK 3 B13 (A**2) : -0.28000 REMARK 3 B23 (A**2) : -0.39000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.058 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.721 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2036 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1893 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2777 ; 1.589 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4369 ; 0.752 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 7.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;31.129 ;24.096 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 318 ;12.875 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;19.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 316 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2337 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 453 ; 0.003 ; 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): 1050 ; 1.088 ; 0.790 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1049 ; 1.087 ; 0.788 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1314 ; 1.506 ; 1.188 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1315 ; 1.507 ; 1.189 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 986 ; 2.239 ; 1.048 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 987 ; 2.238 ; 1.050 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1459 ; 3.278 ; 1.478 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2656 ; 5.024 ; 8.562 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2657 ; 5.023 ; 8.570 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5B15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1300000344. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-15 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 : AICHISR REMARK 200 BEAMLINE : BL2S1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39572 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 40.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.07200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3VPE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, AMMONIUM SULFATE, TRIS REMARK 280 -HYDROCHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 GLN A 1 REMARK 465 ASP A 2 REMARK 465 ARG A 262 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 ND2 ASN A 233 O HOH A 401 1.79 REMARK 500 OD1 ASN A 233 O HOH A 402 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 217 OE1 - CD - OE2 ANGL. DEV. = -7.4 DEGREES 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 ASP A 41 161.99 71.16 REMARK 500 THR A 43 -148.48 61.34 REMARK 500 SER A 73 59.93 -98.85 REMARK 500 CYS A 208 70.32 -150.41 REMARK 500 ASP A 238 97.54 -168.97 REMARK 500 REMARK 500 REMARK: NULL 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 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 9 O REMARK 620 2 ASN A 54 OD1 67.0 REMARK 620 3 HOH A 536 O 86.4 115.1 REMARK 620 4 HOH A 606 O 170.7 111.9 102.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 70 O REMARK 620 2 THR A 71 O 69.7 REMARK 620 3 GLY A 153 O 147.7 85.2 REMARK 620 4 HOH A 499 O 94.5 78.5 100.2 REMARK 620 N 1 2 3 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 72 NE2 REMARK 620 2 HIS A 74 ND1 97.7 REMARK 620 3 HIS A 150 NE2 97.8 100.8 REMARK 620 4 HOH A 425 O 114.6 117.7 123.7 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 76 OD2 REMARK 620 2 HIS A 77 NE2 88.7 REMARK 620 3 HIS A 215 NE2 91.2 92.4 REMARK 620 4 DQM A 313 NAN 100.0 171.1 85.3 REMARK 620 5 DQM A 313 OAE 173.3 98.0 88.2 73.3 REMARK 620 6 HOH A 425 O 93.3 98.9 167.9 82.9 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 82 O REMARK 620 2 GLN A 85 OE1 97.8 REMARK 620 3 HOH A 670 O 125.2 117.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 309 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 98 OD1 REMARK 620 2 THR A 101 OG1 126.4 REMARK 620 3 HOH A 421 O 103.9 123.1 REMARK 620 4 HOH A 533 O 112.3 77.7 58.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 177 O REMARK 620 2 VAL A 179 O 116.7 REMARK 620 3 HOH A 480 O 123.5 100.9 REMARK 620 4 HOH A 570 O 73.0 114.1 128.4 REMARK 620 N 1 2 3 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 ASN A 219 OD1 REMARK 620 2 HOH A 449 O 112.3 REMARK 620 3 HOH A 525 O 107.1 106.9 REMARK 620 4 HOH A 565 O 99.7 101.8 128.8 REMARK 620 5 HOH A 723 O 147.6 52.1 104.9 62.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 308 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SO4 A 311 O1 REMARK 620 2 HOH A 524 O 109.1 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 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 NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQM A 313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AWY RELATED DB: PDB DBREF 5B15 A 1 262 UNP G5ELM3 G5ELM3_SERMA 19 280 SEQRES 1 A 262 GLN ASP ARG ASP TRP SER SER PRO GLN GLN PRO PHE THR SEQRES 2 A 262 ILE TYR GLY ASN THR HIS TYR VAL GLY THR GLY GLY ILE SEQRES 3 A 262 SER ALA VAL LEU LEU SER SER PRO GLN GLY HIS ILE LEU SEQRES 4 A 262 VAL ASP GLY THR THR GLU LYS GLY ALA GLN VAL VAL ALA SEQRES 5 A 262 ALA ASN ILE ARG ALA MET GLY PHE LYS LEU SER ASP VAL SEQRES 6 A 262 LYS TYR ILE LEU SER THR HIS SER HIS GLU ASP HIS ALA SEQRES 7 A 262 GLY GLY ILE SER ALA MET GLN LYS LEU THR GLY ALA THR SEQRES 8 A 262 VAL LEU ALA GLY ALA ALA ASN VAL ASP THR LEU ARG THR SEQRES 9 A 262 GLY VAL SER PRO LYS SER ASP PRO GLN PHE GLY SER LEU SEQRES 10 A 262 SER ASN PHE PRO GLY SER ALA LYS VAL ARG ALA VAL ALA SEQRES 11 A 262 ASP GLY GLU LEU VAL LYS LEU GLY PRO LEU ALA VAL LYS SEQRES 12 A 262 ALA HIS ALA THR PRO GLY HIS THR GLU GLY GLY ILE THR SEQRES 13 A 262 TRP THR TRP GLN SER CYS GLU GLN GLY LYS CYS LYS ASP SEQRES 14 A 262 VAL VAL PHE ALA ASP SER LEU THR ALA VAL SER ALA ASP SEQRES 15 A 262 SER TYR ARG PHE SER ASP HIS PRO GLU VAL VAL ALA SER SEQRES 16 A 262 LEU ARG GLY SER PHE GLU ALA VAL GLU LYS LEU SER CYS SEQRES 17 A 262 ASP ILE ALA ILE ALA ALA HIS PRO GLU VAL ASN ASP MET SEQRES 18 A 262 TRP THR ARG GLN GLN ARG ALA ALA LYS GLU GLY ASN SER SEQRES 19 A 262 ALA TYR VAL ASP ASN GLY ALA CYS ARG ALA ILE ALA ALA SEQRES 20 A 262 ALA GLY ARG LYS ARG LEU GLU THR ARG LEU ALA SER GLU SEQRES 21 A 262 LYS ARG HET ZN A 301 1 HET ZN A 302 1 HET NA A 303 1 HET NA A 304 1 HET NA A 305 1 HET NA A 306 1 HET NA A 307 1 HET NA A 308 1 HET NA A 309 1 HET SO4 A 310 5 HET SO4 A 311 5 HET SO4 A 312 5 HET DQM A 313 28 HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM DQM (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-BIS(OXIDANYL)- HETNAM 2 DQM 1-OXIDANYLIDENE-BUTAN-2-YL]-3-METHYL-4-[(3~{S},5~{S})- HETNAM 3 DQM 5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL]SULFANYL-3, HETNAM 4 DQM 4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLIC ACID HETSYN DQM HYDROLYZED DORIPENEM FORMUL 2 ZN 2(ZN 2+) FORMUL 4 NA 7(NA 1+) FORMUL 11 SO4 3(O4 S 2-) FORMUL 14 DQM C15 H26 N4 O7 S2 FORMUL 15 HOH *340(H2 O) HELIX 1 AA1 LYS A 46 MET A 58 1 13 HELIX 2 AA2 LYS A 61 SER A 63 5 3 HELIX 3 AA3 HIS A 74 GLY A 79 1 6 HELIX 4 AA4 GLY A 80 GLY A 89 1 10 HELIX 5 AA5 ASN A 98 GLY A 105 1 8 HELIX 6 AA6 ARG A 185 ASP A 188 5 4 HELIX 7 AA7 HIS A 189 LEU A 206 1 18 HELIX 8 AA8 HIS A 215 ASN A 219 5 5 HELIX 9 AA9 ASP A 220 GLY A 232 1 13 HELIX 10 AB1 ASN A 233 VAL A 237 5 5 HELIX 11 AB2 GLY A 240 GLU A 260 1 21 SHEET 1 AA1 7 PHE A 12 TYR A 15 0 SHEET 2 AA1 7 THR A 18 TYR A 20 -1 O TYR A 20 N PHE A 12 SHEET 3 AA1 7 VAL A 29 LEU A 31 -1 O LEU A 30 N HIS A 19 SHEET 4 AA1 7 HIS A 37 VAL A 40 -1 O ILE A 38 N LEU A 31 SHEET 5 AA1 7 VAL A 65 LEU A 69 1 O LEU A 69 N LEU A 39 SHEET 6 AA1 7 THR A 91 GLY A 95 1 O LEU A 93 N ILE A 68 SHEET 7 AA1 7 VAL A 126 VAL A 129 1 O ARG A 127 N VAL A 92 SHEET 1 AA2 5 LEU A 134 LEU A 137 0 SHEET 2 AA2 5 LEU A 140 ALA A 146 -1 O VAL A 142 N VAL A 135 SHEET 3 AA2 5 ILE A 155 GLU A 163 -1 O THR A 158 N LYS A 143 SHEET 4 AA2 5 LYS A 166 ALA A 173 -1 O VAL A 170 N TRP A 159 SHEET 5 AA2 5 ILE A 210 ALA A 213 1 O ILE A 212 N VAL A 171 SSBOND 1 CYS A 162 CYS A 167 1555 1555 2.04 SSBOND 2 CYS A 208 CYS A 242 1555 1555 2.04 LINK O GLN A 9 NA NA A 305 1555 1555 3.07 LINK OD1 ASN A 54 NA NA A 305 1555 1555 2.79 LINK O SER A 70 NA NA A 304 1555 1555 2.80 LINK O THR A 71 NA NA A 304 1555 1555 2.98 LINK NE2 HIS A 72 ZN ZN A 301 1555 1555 2.04 LINK ND1 HIS A 74 ZN ZN A 301 1555 1555 2.06 LINK OD2 ASP A 76 ZN ZN A 302 1555 1555 2.13 LINK NE2 HIS A 77 ZN ZN A 302 1555 1555 2.15 LINK O SER A 82 NA NA A 303 1555 1555 3.04 LINK OE1 GLN A 85 NA NA A 303 1555 1555 2.79 LINK OD1 ASN A 98 NA NA A 309 1555 1555 2.88 LINK OG1 THR A 101 NA NA A 309 1555 1555 2.89 LINK NE2 HIS A 150 ZN ZN A 301 1555 1555 2.12 LINK O GLY A 153 NA NA A 304 1555 1555 2.87 LINK O THR A 177 NA NA A 306 1555 1555 3.18 LINK O VAL A 179 NA NA A 306 1555 1555 2.67 LINK NE2 HIS A 215 ZN ZN A 302 1555 1555 2.14 LINK OD1 ASN A 219 NA NA A 307 1555 1555 2.76 LINK ZN ZN A 301 O HOH A 425 1555 1555 1.83 LINK ZN ZN A 302 NAN DQM A 313 1555 1555 2.33 LINK ZN ZN A 302 OAE DQM A 313 1555 1555 2.23 LINK ZN ZN A 302 O HOH A 425 1555 1555 2.08 LINK NA NA A 303 O HOH A 670 1555 1555 2.78 LINK NA NA A 304 O HOH A 499 1555 1555 2.82 LINK NA NA A 305 O HOH A 536 1555 1556 2.80 LINK NA NA A 305 O HOH A 606 1555 1556 2.90 LINK NA NA A 306 O HOH A 480 1555 1555 2.88 LINK NA NA A 306 O HOH A 570 1555 1555 2.62 LINK NA NA A 307 O HOH A 449 1555 1555 2.68 LINK NA NA A 307 O HOH A 525 1555 1555 2.73 LINK NA NA A 307 O HOH A 565 1555 1555 3.03 LINK NA NA A 307 O HOH A 723 1555 1655 2.96 LINK NA NA A 308 O1 SO4 A 311 1555 1555 2.67 LINK NA NA A 308 O HOH A 524 1555 1555 2.75 LINK NA NA A 309 O HOH A 421 1555 1555 2.86 LINK NA NA A 309 O HOH A 533 1555 1555 2.42 SITE 1 AC1 6 HIS A 72 HIS A 74 HIS A 150 ZN A 302 SITE 2 AC1 6 DQM A 313 HOH A 425 SITE 1 AC2 6 ASP A 76 HIS A 77 HIS A 215 ZN A 301 SITE 2 AC2 6 DQM A 313 HOH A 425 SITE 1 AC3 6 SER A 82 GLN A 85 LYS A 86 SER A 123 SITE 2 AC3 6 ALA A 124 HOH A 670 SITE 1 AC4 7 SER A 70 THR A 71 ALA A 94 GLY A 95 SITE 2 AC4 7 GLY A 153 ILE A 155 HOH A 499 SITE 1 AC5 7 PRO A 8 GLN A 9 VAL A 50 ASN A 54 SITE 2 AC5 7 PRO A 190 HOH A 536 HOH A 606 SITE 1 AC6 5 HIS A 150 THR A 177 VAL A 179 HOH A 480 SITE 2 AC6 5 HOH A 570 SITE 1 AC7 5 ASN A 219 HOH A 449 HOH A 525 HOH A 565 SITE 2 AC7 5 HOH A 723 SITE 1 AC8 5 ARG A 103 LYS A 125 VAL A 126 SO4 A 311 SITE 2 AC8 5 HOH A 524 SITE 1 AC9 7 SER A 73 ALA A 97 ASN A 98 THR A 101 SITE 2 AC9 7 PRO A 108 HOH A 421 HOH A 533 SITE 1 AD1 10 LYS A 125 ARG A 127 THR A 177 ARG A 252 SITE 2 AD1 10 HOH A 407 HOH A 429 HOH A 447 HOH A 458 SITE 3 AD1 10 HOH A 476 HOH A 520 SITE 1 AD2 8 ALA A 124 LYS A 125 ARG A 127 ARG A 252 SITE 2 AD2 8 NA A 308 HOH A 465 HOH A 563 HOH A 577 SITE 1 AD3 6 LYS A 61 LEU A 62 SER A 63 HOH A 436 SITE 2 AD3 6 HOH A 487 HOH A 491 SITE 1 AD4 20 TRP A 5 ASP A 76 HIS A 77 GLY A 89 SITE 2 AD4 20 GLN A 113 LYS A 125 HIS A 150 SER A 175 SITE 3 AD4 20 THR A 177 HIS A 215 GLU A 217 ARG A 252 SITE 4 AD4 20 ZN A 301 ZN A 302 HOH A 403 HOH A 425 SITE 5 AD4 20 HOH A 526 HOH A 591 HOH A 595 HOH A 620 CRYST1 37.010 40.920 45.320 107.57 102.56 107.01 P 1 1 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 0.027020 0.008266 0.010060 0.00000 SCALE2 0.000000 0.025556 0.010876 0.00000 SCALE3 0.000000 0.000000 0.024568 0.00000