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Yorodumi- PDB-5axr: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-merc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5axr | ||||||
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Title | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-mercaptoethanesulfonate | ||||||
Components | Metallo-beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wachino, J. / Arakawa, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-mercaptoethanesulfonate Authors: Wachino, J. / Arakawa, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5axr.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5axr.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 5axr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5axr_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 5axr_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 5axr_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5axr_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5axr ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5axr | HTTPS FTP |
-Related structure data
Related structure data | 3vpeS 5awy 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: 27754.043 Da / Num. of mol.: 1 / Fragment: UNP residues 19-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: SMB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5ELM3, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-COM / | #5: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Lithium Chloride, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→58.13 Å / Num. obs: 13741 / % possible obs: 100 % / Redundancy: 11.6 % / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 10.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VPE Resolution: 2.1→58.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.455 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 22.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→58.12 Å
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Refine LS restraints |
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