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Yorodumi- PDB-1ghm: Structures of the acyl-enzyme complex of the staphylococcus aureu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ghm | ||||||
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Title | Structures of the acyl-enzyme complex of the staphylococcus aureus beta-lactamase mutant GLU166ASP:ASN170GLN with degraded cephaloridine | ||||||
Components | BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / BETA-LACTAM HYDROLYSIS / BENZYLPENICILLIN / CEPHALORIDINE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å | ||||||
Authors | Chen, C.C.H. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structures of the acyl-enzyme complexes of the Staphylococcus aureus beta-lactamase mutant Glu166Asp:Asn170Gln with benzylpenicillin and cephaloridine. Authors: Chen, C.C. / Herzberg, O. #1: Journal: Protein Eng. / Year: 1995 Title: An Engineered Staphylococcus Aureus Pc1 Beta-Lactamase that Hydrolyses Third-Generation Cephalosporins Authors: Zawadzke, L.E. / Smith, T.J. / Herzberg, O. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 Authors: Herzberg, O. #3: Journal: Science / Year: 1987 Title: Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution Authors: Herzberg, O. / Moult, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ghm.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ghm.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ghm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ghm_validation.pdf.gz | 891.1 KB | Display | wwPDB validaton report |
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Full document | 1ghm_full_validation.pdf.gz | 897 KB | Display | |
Data in XML | 1ghm_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1ghm_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/1ghm ftp://data.pdbj.org/pub/pdb/validation_reports/gh/1ghm | HTTPS FTP |
-Related structure data
Related structure data | 1ghiC 1ghpC 1djcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28974.410 Da / Num. of mol.: 1 / Mutation: E166D, N170Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: PC1 / Gene: BLAZ / Plasmid: PTS32 / Gene (production host): BLAZ / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00807, beta-lactamase | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CO3 / | #4: Chemical | ChemComp-CED / | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal amounts of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 15, 1998 / Details: MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→21.8 Å / Num. obs: 31672 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.6 / % possible all: 96.9 |
Reflection shell | *PLUS % possible obs: 96.9 % / Num. unique obs: 3077 |
-Processing
Software |
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Refinement | Starting model: 1DJC Resolution: 1.86→21.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.86→21.8 Å
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Refine LS restraints |
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