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Yorodumi- PDB-5ihv: Crystal structure of a beta-lactamase from Burkholderia ambifaria -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ihv | ||||||
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Title | Crystal structure of a beta-lactamase from Burkholderia ambifaria | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / SSGCID / beta-lactamase / Burkholderia ambifaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Burkholderia ambifaria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal structure of a beta-lactamase from Burkholderia ambifaria Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ihv.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ihv.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ihv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ihv_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 5ihv_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 5ihv_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5ihv_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ihv ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ihv | HTTPS FTP |
-Related structure data
Related structure data | 3w4qS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28190.980 Da / Num. of mol.: 1 / Fragment: UNP residues 39-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: BamMC406_4487 / Plasmid: BuamA.00104.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YX81, beta-lactamase | ||
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#2: Chemical | #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: 2.04 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: JCSG+ A7 (267021a7): 100mM CHES pH 9.5, 20% PEG8000, protein conc. 48.83mg/mL; cryo 20% EG; puck uqf3-6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 20, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→50 Å / Num. obs: 92835 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 9.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3w4q Resolution: 1.1→50 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.34 Å2 / Biso mean: 15.5674 Å2 / Biso min: 5.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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