HEADER HYDROLASE 02-NOV-17 5YPL
TITLE CRYSTAL STRUCTURE OF NDM-1 BOUND TO HYDROLYZED IMIPENEM REPRESENTING
TITLE 2 AN EP COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: METALLO-BETA-LACTAMASE NDM-1;
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-1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS NDM-1, IMIPENEM, EP COMPLEX, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.FENG,D.WANG,W.LIU
REVDAT 2 22-NOV-23 5YPL 1 COMPND HETNAM LINK
REVDAT 1 21-FEB-18 5YPL 0
JRNL AUTH H.FENG,X.LIU,S.WANG,J.FLEMING,D.C.WANG,W.LIU
JRNL TITL THE MECHANISM OF NDM-1-CATALYZED CARBAPENEM HYDROLYSIS IS
JRNL TITL 2 DISTINCT FROM THAT OF PENICILLIN OR CEPHALOSPORIN
JRNL TITL 3 HYDROLYSIS.
JRNL REF NAT COMMUN V. 8 2242 2017
JRNL REFN ESSN 2041-1723
JRNL PMID 29269938
JRNL DOI 10.1038/S41467-017-02339-W
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.28
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 3 NUMBER OF REFLECTIONS : 35229
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.171
REMARK 3 R VALUE (WORKING SET) : 0.169
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.680
REMARK 3 FREE R VALUE TEST SET COUNT : 3792
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.730
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE FACTOR FILE CONTAINS
REMARK 3 FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
REMARK 4
REMARK 4 5YPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-17.
REMARK 100 THE DEPOSITION ID IS D_1300005665.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-MAY-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 : 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) : 0.97845
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 : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35229
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 42.280
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 200 DATA REDUNDANCY : 6.360
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84
REMARK 200 COMPLETENESS FOR SHELL (%) : 64.8
REMARK 200 DATA REDUNDANCY IN SHELL : 4.44
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.55500
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.550
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 4RL0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 36.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 28% (W/V) PEG3350, 0.1M BIS-TRIS, PH
REMARK 280 5.8, 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 295K
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 34.61000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.71500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.88000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.71500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.61000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.88000
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 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9790 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9600 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
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 29
REMARK 465 GLU A 30
REMARK 465 ILE A 31
REMARK 465 ARG A 32
REMARK 465 PRO A 33
REMARK 465 THR A 34
REMARK 465 ILE A 35
REMARK 465 GLY A 36
REMARK 465 GLN A 37
REMARK 465 GLN A 38
REMARK 465 MET A 39
REMARK 465 GLU A 40
REMARK 465 THR A 41
REMARK 465 GLY B 29
REMARK 465 GLU B 30
REMARK 465 ILE B 31
REMARK 465 ARG B 32
REMARK 465 PRO B 33
REMARK 465 THR B 34
REMARK 465 ILE B 35
REMARK 465 GLY B 36
REMARK 465 GLN B 37
REMARK 465 GLN B 38
REMARK 465 MET B 39
REMARK 465 GLU B 40
REMARK 465 THR B 41
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 589 O HOH A 591 1.02
REMARK 500 O HOH A 531 O HOH A 547 1.12
REMARK 500 O HOH A 528 O HOH A 535 1.26
REMARK 500 O HOH B 456 O HOH B 477 1.35
REMARK 500 O HOH B 532 O HOH B 552 1.49
REMARK 500 N ALA B 215 O HOH B 401 1.52
REMARK 500 O HOH A 449 O HOH A 569 1.58
REMARK 500 O HOH A 578 O HOH B 540 1.61
REMARK 500 N LEU B 221 O HOH B 402 1.67
REMARK 500 C ASN B 220 O HOH B 402 1.77
REMARK 500 NZ LYS B 242 O HOH B 403 1.83
REMARK 500 O HOH B 548 O HOH B 567 1.85
REMARK 500 O PRO A 241 O HOH A 401 1.85
REMARK 500 C LYS B 214 O HOH B 401 1.97
REMARK 500 O GLY B 219 O HOH B 402 2.01
REMARK 500 OG SER A 251 O HOH A 402 2.02
REMARK 500 O GLY A 219 O HOH A 403 2.02
REMARK 500 OE1 GLU A 227 O HOH A 404 2.08
REMARK 500 O LYS B 242 O HOH B 404 2.11
REMARK 500 O HOH B 519 O HOH B 522 2.15
REMARK 500 O HOH B 492 O HOH B 513 2.16
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 90 144.50 73.40
REMARK 500 ASP B 90 145.78 75.02
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 589 DISTANCE = 5.87 ANGSTROMS
REMARK 525 HOH A 590 DISTANCE = 5.89 ANGSTROMS
REMARK 525 HOH A 591 DISTANCE = 6.07 ANGSTROMS
REMARK 525 HOH A 592 DISTANCE = 6.55 ANGSTROMS
REMARK 525 HOH A 593 DISTANCE = 7.41 ANGSTROMS
REMARK 525 HOH B 577 DISTANCE = 6.03 ANGSTROMS
REMARK 525 HOH B 578 DISTANCE = 7.91 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 96.4
REMARK 620 3 HIS A 189 NE2 106.0 113.5
REMARK 620 4 HIW A 303 O72 127.9 108.1 105.0
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 105.1
REMARK 620 3 HIS A 250 NE2 95.6 111.8
REMARK 620 4 HIW A 303 O72 97.6 101.5 139.4
REMARK 620 5 HIW A 303 N4 115.4 138.4 74.5 65.2
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 105.0
REMARK 620 3 HIS B 189 NE2 107.4 110.6
REMARK 620 4 HIW B 303 O71 121.7 101.8 110.0
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 95.6
REMARK 620 3 HIS B 250 NE2 96.6 106.6
REMARK 620 4 HIW B 303 N4 115.8 147.8 78.1
REMARK 620 5 HIW B 303 O71 94.8 104.0 146.1 68.1
REMARK 620 N 1 2 3 4
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 HIW A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue HIW B 303
DBREF1 5YPL A 29 270 UNP A0A0A7Y424_ECOLX
DBREF2 5YPL A A0A0A7Y424 23 264
DBREF1 5YPL B 29 270 UNP A0A0A7Y424_ECOLX
DBREF2 5YPL B A0A0A7Y424 23 264
SEQRES 1 A 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR
SEQRES 2 A 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU
SEQRES 3 A 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET
SEQRES 4 A 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL
SEQRES 5 A 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP
SEQRES 6 A 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS
SEQRES 7 A 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR
SEQRES 8 A 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU
SEQRES 9 A 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER
SEQRES 10 A 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN
SEQRES 11 A 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO
SEQRES 12 A 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR
SEQRES 13 A 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY
SEQRES 14 A 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE
SEQRES 15 A 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP
SEQRES 16 A 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE
SEQRES 17 A 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER
SEQRES 18 A 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR
SEQRES 19 A 242 ALA ARG MET ALA ASP LYS LEU ARG
SEQRES 1 B 242 GLY GLU ILE ARG PRO THR ILE GLY GLN GLN MET GLU THR
SEQRES 2 B 242 GLY ASP GLN ARG PHE GLY ASP LEU VAL PHE ARG GLN LEU
SEQRES 3 B 242 ALA PRO ASN VAL TRP GLN HIS THR SER TYR LEU ASP MET
SEQRES 4 B 242 PRO GLY PHE GLY ALA VAL ALA SER ASN GLY LEU ILE VAL
SEQRES 5 B 242 ARG ASP GLY GLY ARG VAL LEU VAL VAL ASP THR ALA TRP
SEQRES 6 B 242 THR ASP ASP GLN THR ALA GLN ILE LEU ASN TRP ILE LYS
SEQRES 7 B 242 GLN GLU ILE ASN LEU PRO VAL ALA LEU ALA VAL VAL THR
SEQRES 8 B 242 HIS ALA HIS GLN ASP LYS MET GLY GLY MET ASP ALA LEU
SEQRES 9 B 242 HIS ALA ALA GLY ILE ALA THR TYR ALA ASN ALA LEU SER
SEQRES 10 B 242 ASN GLN LEU ALA PRO GLN GLU GLY MET VAL ALA ALA GLN
SEQRES 11 B 242 HIS SER LEU THR PHE ALA ALA ASN GLY TRP VAL GLU PRO
SEQRES 12 B 242 ALA THR ALA PRO ASN PHE GLY PRO LEU LYS VAL PHE TYR
SEQRES 13 B 242 PRO GLY PRO GLY HIS THR SER ASP ASN ILE THR VAL GLY
SEQRES 14 B 242 ILE ASP GLY THR ASP ILE ALA PHE GLY GLY CYS LEU ILE
SEQRES 15 B 242 LYS ASP SER LYS ALA LYS SER LEU GLY ASN LEU GLY ASP
SEQRES 16 B 242 ALA ASP THR GLU HIS TYR ALA ALA SER ALA ARG ALA PHE
SEQRES 17 B 242 GLY ALA ALA PHE PRO LYS ALA SER MET ILE VAL MET SER
SEQRES 18 B 242 HIS SER ALA PRO ASP SER ARG ALA ALA ILE THR HIS THR
SEQRES 19 B 242 ALA ARG MET ALA ASP LYS LEU ARG
HET ZN A 301 1
HET ZN A 302 1
HET HIW A 303 21
HET SO4 A 304 5
HET ZN B 301 1
HET ZN B 302 1
HET HIW B 303 21
HET CL B 304 1
HETNAM ZN ZINC ION
HETNAM HIW (2R,4S)-2-[(1S,2R)-1-CARBOXY-2-HYDROXYPROPYL]-4-[(2-
HETNAM 2 HIW {[(Z)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-3,4-DIHYDRO-
HETNAM 3 HIW 2H-PYRROLE-5-CA RBOXYLIC ACID
HETNAM SO4 SULFATE ION
HETNAM CL CHLORIDE ION
HETSYN HIW HYDROLYZED IMIPENEM
FORMUL 3 ZN 4(ZN 2+)
FORMUL 5 HIW 2(C12 H19 N3 O5 S)
FORMUL 6 SO4 O4 S 2-
FORMUL 10 CL CL 1-
FORMUL 11 HOH *371(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 LEU A 87 N VAL A 80
SHEET 6 AA1 8 VAL A 113 VAL A 118 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 VAL A 118
SHEET 8 AA1 8 HIS A 159 LEU A 161 1 O LEU A 161 N ALA A 141
SHEET 1 AA2 5 LEU A 180 PHE A 183 0
SHEET 2 AA2 5 THR A 195 ILE A 198 -1 O GLY A 197 N LYS A 181
SHEET 3 AA2 5 ILE A 203 GLY A 207 -1 O PHE A 205 N VAL A 196
SHEET 4 AA2 5 MET A 245 MET A 248 1 O VAL A 247 N GLY A 206
SHEET 5 AA2 5 SER A 251 ASP A 254 -1 O ASP A 254 N ILE A 246
SHEET 1 AA3 8 GLN B 44 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 VAL B 73 N LEU B 65
SHEET 5 AA3 8 ARG B 85 VAL B 89 -1 O ARG B 85 N ASP B 82
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 5 LEU B 180 PHE B 183 0
SHEET 2 AA4 5 THR B 195 ILE B 198 -1 O GLY B 197 N LYS B 181
SHEET 3 AA4 5 ILE B 203 GLY B 207 -1 O PHE B 205 N VAL B 196
SHEET 4 AA4 5 MET B 245 MET B 248 1 O VAL B 247 N ALA B 204
SHEET 5 AA4 5 SER B 251 ASP B 254 -1 O ASP B 254 N ILE B 246
LINK NE2 HIS A 120 ZN ZN A 301 1555 1555 2.13
LINK ND1 HIS A 122 ZN ZN A 301 1555 1555 2.03
LINK OD2 ASP A 124 ZN ZN A 302 1555 1555 2.04
LINK NE2 HIS A 189 ZN ZN A 301 1555 1555 2.07
LINK SG CYS A 208 ZN ZN A 302 1555 1555 2.30
LINK NE2 HIS A 250 ZN ZN A 302 1555 1555 2.07
LINK ZN ZN A 301 O72 HIW A 303 1555 1555 2.07
LINK ZN ZN A 302 O72 HIW A 303 1555 1555 2.46
LINK ZN ZN A 302 N4 HIW A 303 1555 1555 2.40
LINK NE2 HIS B 120 ZN ZN B 301 1555 1555 2.12
LINK ND1 HIS B 122 ZN ZN B 301 1555 1555 1.95
LINK OD2 ASP B 124 ZN ZN B 302 1555 1555 2.06
LINK NE2 HIS B 189 ZN ZN B 301 1555 1555 2.03
LINK SG CYS B 208 ZN ZN B 302 1555 1555 2.29
LINK NE2 HIS B 250 ZN ZN B 302 1555 1555 2.09
LINK ZN ZN B 301 O71 HIW B 303 1555 1555 2.08
LINK ZN ZN B 302 N4 HIW B 303 1555 1555 2.16
LINK ZN ZN B 302 O71 HIW B 303 1555 1555 2.52
SITE 1 AC1 4 HIS A 120 HIS A 122 HIS A 189 HIW A 303
SITE 1 AC2 4 ASP A 124 CYS A 208 HIS A 250 HIW A 303
SITE 1 AC3 11 HIS A 122 ASP A 124 HIS A 189 CYS A 208
SITE 2 AC3 11 LYS A 211 GLY A 219 ASN A 220 HIS A 250
SITE 3 AC3 11 ZN A 301 ZN A 302 GLY B 69
SITE 1 AC4 3 ARG A 234 THR A 260 ARG A 264
SITE 1 AC5 4 HIS B 120 HIS B 122 HIS B 189 HIW B 303
SITE 1 AC6 4 ASP B 124 CYS B 208 HIS B 250 HIW B 303
SITE 1 AC7 13 GLY A 69 PHE A 70 TRP B 93 HIS B 120
SITE 2 AC7 13 HIS B 122 ASP B 124 HIS B 189 LYS B 211
SITE 3 AC7 13 GLY B 219 ASN B 220 HIS B 250 ZN B 301
SITE 4 AC7 13 ZN B 302
CRYST1 69.220 73.760 77.430 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 0.014447 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013557 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012915 0.00000