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Yorodumi- PDB-3cg5: Crystal Structure of the Covalent Adduct Formed between TB B-lact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cg5 | ||||||
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Title | Crystal Structure of the Covalent Adduct Formed between TB B-lactamase and Clavulanate | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / alpha-beta structure / covalent adduct / Antibiotic resistance / Lipoprotein / Membrane / Palmitate | ||||||
Function / homology | Function and homology information : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tremblay, L.W. / Hugonnet, J.E. / Blanchard, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structure of the covalent adduct formed between Mycobacterium tuberculosis beta-lactamase and clavulanate. Authors: Tremblay, L.W. / Hugonnet, J.E. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cg5.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cg5.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cg5_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 3cg5_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 3cg5_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3cg5_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cg5 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cg5 | HTTPS FTP |
-Related structure data
Related structure data | 2gdnS 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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Unit cell |
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-Components
#1: Protein | Mass: 28272.721 Da / Num. of mol.: 1 / Fragment: UNP residues 43-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-ISS / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | CLAVULANATE WAS USED IN PROTEIN SOLUTION WHICH UNDERWENT CHEMICAL REACTION AND SUBSEQUENTLY FORMED ...CLAVULANAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 0.1 M HEPES pH 7.5, 2 M NH4(H2)PO4, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2007 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.4 Å / Num. all: 27349 / Num. obs: 27349 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15.76 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 1732 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GDN Resolution: 1.7→41.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.54 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.99 Å2
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Refine analyze | Luzzati sigma a obs: 0.1947 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→41.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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