+Open data
-Basic information
Entry | Database: PDB / ID: 4yfm | ||||||
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Title | Class A beta-lactamase from Mycobacterium abscessus | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / clavulanate / carbapenem / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycobacterium abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Soroka, D. / Li de la Sierra-Gallay, I. / Dubee, V. / van Tilbeurgh, H. / Arthur, M. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 Title: Hydrolysis of Clavulanate by Mycobacterium tuberculosis beta-Lactamase BlaC Harboring a Canonical SDN Motif. Authors: Soroka, D. / Li de la Sierra-Gallay, I. / Dubee, V. / Triboulet, S. / van Tilbeurgh, H. / Compain, F. / Ballell, L. / Barros, D. / Mainardi, J.L. / Hugonnet, J.E. / Arthur, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yfm.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yfm.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 4yfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yfm_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 4yfm_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 4yfm_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 4yfm_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfm ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfm | HTTPS FTP |
-Related structure data
Related structure data | 2gdnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30133.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: LA62_14585 / Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: A0A089SRR3, UniProt: B1MCI3*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium acetate, 0.1 MES (pH 6.5), 32% polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.5 Å / Num. obs: 93890 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.29 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.34 / % possible all: 73.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDN Resolution: 1.4→41.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.224 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.055 / 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: 18.543 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→41.45 Å
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Refine LS restraints |
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