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Yorodumi- PDB-2h6a: Crystal structure of the zinc-beta-lactamase L1 from Stenotrophom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6a | ||||||
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Title | Crystal structure of the zinc-beta-lactamase L1 from Stenotrophomonas maltophilia (mono zinc form) | ||||||
Components | Metallo-beta-lactamase L1 | ||||||
Keywords | HYDROLASE / METALLO / ZN / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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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Remark 999 | SEQUENCE THESE COORDINATES CONTAIN NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY ...SEQUENCE THESE COORDINATES CONTAIN NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY (SEE REFERENCE 1). Residue B THR 57 and Residue B GLU 67 are not linked. The length of the C-N(B) bond is 1.77A. Also, residue B ARG 276 and residue B ALA 289 are not linked. The C(A)-N bond is 2.42A. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6a.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6a.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 2h6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6a ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6a | HTTPS FTP |
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-Related structure data
Related structure data | 2fm6C 2fu7C 2fu8C 2fu9C 2gfjC 2gfkC 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
#1: Protein | Mass: 28740.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P52700, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | 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: 2.54 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AS, SOAKED CRYSTAL IN 5 ML DROP WITH CRYSTALLIZATION CONDITIONS AND 0.005 M EDTA FOR 30 MINUTES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: Xenocs multilayers |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.74 Å / Num. obs: 57235 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.372 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SML Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.254 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue B THR 57 and Residue B GLU 67 are not linked. The bond length of the C-N(B) bond is 1.77. Also, residue B ARG 276 and residue B ALA ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue B THR 57 and Residue B GLU 67 are not linked. The bond length of the C-N(B) bond is 1.77. Also, residue B ARG 276 and residue B ALA 289 are not linked. The C(A)-N bond is 2.42.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.145 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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