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Yorodumi- PDB-1zc2: Crystal Structure of plasmid-encoded class C beta-lactamase CMY-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zc2 | ||||||
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Title | Crystal Structure of plasmid-encoded class C beta-lactamase CMY-2 complexed with citrate molecule | ||||||
Components | beta-lactamase class C | ||||||
Keywords | HYDROLASE / beta-lactamase cephalosporinase / AMPC-type / serine hydrolase / citrate | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Bauvois, C. / Jacquamet, L. / Fieulaine, S. / Frere, J.-M. / Galleni, M. / Ferrer, J.-L. | ||||||
Citation | Journal: To be Published Title: Crystallographic structure of plasmid-encoded CMY-2 beta-lactamase revealed citrate molecule in the active site. Authors: Bauvois, C. / Jacquamet, L. / Fieulaine, S. / Frere, J.-M. / Galleni, M. / Ferrer, J.-L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zc2.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zc2.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zc2 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zc2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39896.492 Da / Num. of mol.: 2 / Fragment: residues 1-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla CMY-2 / Plasmid: pET26b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q48434, beta-lactamase #2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: citric acid 0.1M, PEG 6000 30 % w/v, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979565 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 4, 2004 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979565 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→43.85 Å / Num. all: 44320 / Num. obs: 43482 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.09→2.21 Å / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→43.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.538 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.284 / ESU R Free: 0.243 / 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: 19.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→43.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 Å / Total num. of bins used: 20
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