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Yorodumi- PDB-2fu7: Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (Cu-subs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fu7 | ||||||
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Title | Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (Cu-substituted form) | ||||||
Components | Metallo-beta-lactamase L1 | ||||||
Keywords | HYDROLASE / ZN / METALLO / BETA / LACTAMASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Nauton, L. / Garau, G. / Kahn, R. / Dideberg, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia. Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O. #1: Journal: Embo J. / Year: 1995 Title: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O. #2: Journal: J.Mol.Biol. / Year: 2005 Title: A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fu7.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fu7.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fu7 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fu7 | HTTPS FTP |
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-Related structure data
Related structure data | 2fm6C 2fu8C 2fu9C 2gfjC 2gfkC 2h6aC 2hb9C 1smlS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28740.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Strain: IID 1275 / Cellular location: PERIPLASM / Gene: L1 / Plasmid details: PUB 5832 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase |
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-Non-polymers , 5 types, 463 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979667 / Wavelength: 0.979667 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979667 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.42 Å / Num. obs: 55212 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.445 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SML Resolution: 1.85→46.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.426 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→46.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20 /
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