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Yorodumi- PDB-2qin: Stenotrophomonas maltophilia L1 Metallo-beta-Lactamase Asp-120 Cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qin | ||||||
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Title | Stenotrophomonas maltophilia L1 Metallo-beta-Lactamase Asp-120 Cys mutant | ||||||
Components | Metallo-beta-lactamase L1 | ||||||
Keywords | HYDROLASE / METALLO-BETA-LACTAMASE / BINUCLEAR / DINUCLEAR | ||||||
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: 1.76 Å | ||||||
Authors | Spencer, J. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural Basis for the Role of Asp-120 in Metallo-beta-lactamases. Authors: Crisp, J. / Conners, R. / Garrity, J.D. / Carenbauer, A.L. / Crowder, M.W. / Spencer, J. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Metal Binding Asp-120 in Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia Plays a Crucial Role in Catalysis Authors: Garrity, J.D. / Carenbauer, A.L. / Herron, L.R. / Crowder, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qin.cif.gz | 236.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qin.ent.gz | 185.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qin_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 2qin_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 2qin_validation.xml.gz | 50.2 KB | Display | |
Data in CIF | 2qin_validation.cif.gz | 76.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/2qin ftp://data.pdbj.org/pub/pdb/validation_reports/qi/2qin | HTTPS FTP |
-Related structure data
Related structure data | 2qjsC 1smlS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28728.508 Da / Num. of mol.: 4 / Mutation: D120C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Strain: IID 1275 / Gene: L1 / Plasmid: pUB5832 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P52700, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris.Cl, 0.2M MgCl2, 18% PEG 4000, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. all: 104385 / Num. obs: 98730 / % possible obs: 94.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 18.795 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.76→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7 / Num. unique all: 13052 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SML Resolution: 1.76→26.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.187 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→26.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.759→1.805 Å / Total num. of bins used: 20
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