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Yorodumi- PDB-9bzq: Structure of Class A Beta-lactamase from Bordetella bronchiseptic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bzq | ||||||
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Title | Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam | ||||||
Components | class A Beta-lactamase, PenP superfamily | ||||||
Keywords | HYDROLASE / lactamase / serine hydrolase / PenP / CSBID / Center for Structural Biology of Infectious Diseases / Avibactam | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Bordetella bronchiseptica RB50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of Class A Beta-lactamase from Bordetella bronchiseptica RB50 in a complex with Avibactam Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bzq.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bzq.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 9bzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bzq_validation.pdf.gz | 778 KB | Display | wwPDB validaton report |
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Full document | 9bzq_full_validation.pdf.gz | 778.2 KB | Display | |
Data in XML | 9bzq_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 9bzq_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/9bzq ftp://data.pdbj.org/pub/pdb/validation_reports/bz/9bzq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28914.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria) Gene: BB2049 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0H3LUA9, beta-lactamase |
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-Non-polymers , 5 types, 311 molecules
#2: Chemical | ChemComp-NXL / ( |
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#3: Chemical | ChemComp-SIN / |
#4: Chemical | ChemComp-FMT / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Succinic acid pH 7.0; 15% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. obs: 39292 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Net I/σ(I): 48.8 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Num. unique obs: 1936 / CC1/2: 0.992 / Rpim(I) all: 0.04 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→26.01 Å / SU ML: 0.1089 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 13.6027 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→26.01 Å
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Refine LS restraints |
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LS refinement shell |
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