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Open data
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Basic information
Entry | Database: PDB / ID: 3o3v | ||||||
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Title | Crystal structure of ClbP peptidase domain | ||||||
![]() | beta-lactamase | ||||||
![]() | HYDROLASE / alpha/beta / disulfide bridge | ||||||
Function / homology | Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dubois, D. / Cougnoux, A. / Delmas, J. / Bonnet, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.3 KB | Display | ![]() |
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PDB format | ![]() | 163.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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 |
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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.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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