+Open data
-Basic information
Entry | Database: PDB / ID: 5ctm | ||||||
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Title | Structure of BPu1 beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Bacillus pumilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å | ||||||
Authors | Smith, C.A. / Vakulenko, S.B. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Class D beta-lactamases do exist in Gram-positive bacteria. Authors: Toth, M. / Antunes, N.T. / Stewart, N.K. / Frase, H. / Bhattacharya, M. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ctm.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ctm.ent.gz | 287.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ctm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ctm_validation.pdf.gz | 487.6 KB | Display | wwPDB validaton report |
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Full document | 5ctm_full_validation.pdf.gz | 494.6 KB | Display | |
Data in XML | 5ctm_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 5ctm_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/5ctm ftp://data.pdbj.org/pub/pdb/validation_reports/ct/5ctm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27341.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BPUM_2340 / Production host: Escherichia coli (E. coli) / References: UniProt: A8FFI9, beta-lactamase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: 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: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 2% Tacsimate (pH 5.0), 0.1 M sodium citrate pH 5.6, 16% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1→64.9 Å / Num. obs: 261147 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→37.696 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.46 Å2 / Biso mean: 17.5944 Å2 / Biso min: 6.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1→37.696 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: 30 / % reflection obs: 100 %
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