+Open data
-Basic information
Entry | Database: PDB / ID: 3o3v | ||||||
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Title | Crystal structure of ClbP peptidase domain | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / alpha/beta / disulfide bridge | ||||||
Function / homology | Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Dubois, D. / Cougnoux, A. / Delmas, J. / Bonnet, R. | ||||||
Citation | Journal: To be Published Title: ClbP x-ray structure, the prototype of a peptidase family associated to NRP production Authors: Dubois, D. / Baron, O. / Cougnoux, A. / Delmas, J. / Pradel, N. / Nougayrede, J.P. / Robin, F. / Oswald, E. / Bonnet, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3v.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3v.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3v ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3v | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | BIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS |
-Components
#1: Protein | Mass: 36800.004 Da / Num. of mol.: 3 / Fragment: UNP residues 38-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: IHE3034 / Gene: clbp, ECOK1_2171 / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5D5I9, beta-lactamase #2: 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: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: potassium phosphate 1.2M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.94 Å / Num. obs: 39793 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Redundancy: 3 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.384 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2894 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.94 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2565 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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