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- PDB-2vyu: CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vyu | ||||||
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Title | CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE IN THE PRESENCE OF A PEPTIDOGLYCAN ANALOGUE (TETRASACCHARIDE-PENTAPEPTIDE) | ||||||
![]() | CHOLINE BINDING PROTEIN F | ||||||
![]() | CHOLINE-BINDING PROTEIN / CBPF / PEPTIDOGLYCAN / CHOLINE-BINDING-PROTEIN / LIPID-BINDING PROTEIN | ||||||
Function / homology | ![]() left handed beta-beta-3-solenoid - #20 / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perez-Dorado, I. / Molina, R. / Hermoso, J.A. / Mobashery, S. | ||||||
![]() | ![]() Title: Crystal Structure of Cbpf, a Bifunctional Choline-Binding Protein and Autolysis Regulator from Streptococcus Pneumoniae. Authors: Molina, R. / Gonzalez, A. / Stelter, M. / Perez-Dorado, I. / Kahn, R. / Morales, M. / Campuzano, S. / Campillo, N.E. / Mobashery, S. / Garcia, J.L. / Garcia, P. / Hermoso, J.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Choline-Binding Protein F from Streptococcus Pneumoniae. Authors: Molina, R. / Gonzalez, A. / Moscoso, M. / Garcia, P. / Stelter, M. / Kahn, R. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.6 KB | Display | ![]() |
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PDB format | ![]() | 61.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 446.6 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v04C ![]() 2v05S C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 39383.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CHT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953746 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.2 Å / Num. obs: 26724 / % possible obs: 84 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.45→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 7.9 / % possible all: 87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V05 Resolution: 2.45→41.84 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES FROM 168 TO 178 ARE DISORDERED SO THEY DO NOT APPEAR IN THE MODEL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.79 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→41.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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