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Yorodumi- PDB-2v04: CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v04 | ||||||
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Title | CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE | ||||||
Components | CHOLINE BINDING PROTEIN F | ||||||
Keywords | LIPID BINDING PROTEIN / CBPF / CHOLINE-BINDING-PROTEIN / LIPID-BINDING-PROTEIN | ||||||
Function / homology | Function and homology information 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 | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Hermoso, J. / Molina, R. / Kahn, R. / Stelter, M. | ||||||
Citation | Journal: Embo Rep. / Year: 2009 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v04.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v04.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/2v04 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/2v04 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36322.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8DR52 | ||
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#2: Chemical | ChemComp-CHT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 21, 2003 / Details: DOUBLE-MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.92 Å / Num. obs: 25934 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.1→26.92 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.868 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.182 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→26.92 Å
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Refine LS restraints |
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