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Yorodumi- PDB-3qhy: Structural, thermodynamic and kinetic analysis of the picomolar b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qhy | ||||||
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Title | Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / enyzme-inhibitor complex / beta-propeller / beta-lactamase / protein:protein interaction / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) Streptomyces exfoliatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Brown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V.V. / Palzkill, T. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Analysis of the binding forces driving the tight interactions between beta-lactamase inhibitory protein-II (BLIP-II) and class A beta-lactamases. Authors: Brown, N.G. / Chow, D.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qhy.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qhy.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qhy ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qhy | HTTPS FTP |
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-Related structure data
Related structure data | 3qi0C 1jtdS 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
#1: Protein | Mass: 29759.611 Da / Num. of mol.: 1 / Fragment: unp residues 39-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: bla1, BA_2507, GBAA2507, GBAA_2507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93T42, beta-lactamase |
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#2: Protein | Mass: 28360.947 Da / Num. of mol.: 1 / Fragment: unp residues 41-311 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: bliB / Production host: Escherichia coli (E. coli) / References: UniProt: O87916 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 0.1M Bicine, 13 % PEG 10,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2010 |
Radiation | Monochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 37880 / % possible obs: 98.4 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.06→2.1 Å / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JTD Resolution: 2.06→49.95 Å / SU ML: 0.26 / σ(F): 1.93 / Phase error: 20.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.74 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.06→49.95 Å
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Refine LS restraints |
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LS refinement shell |
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