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Yorodumi- PDB-2v05: CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v05 | ||||||
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Title | CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE. CRYSTAL FORM II. | ||||||
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 / SAD / Resolution: 1.67 Å | ||||||
Authors | Hermoso, J. / Molina, R. / Kahn, R. / Stelter, M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Choline Binding Protein F from Streptococcus Pneumoniae Authors: Hermoso, J. / Molina, R. / Gonzalez, A. / Stelter, M. / Garcia, P. / Kahn, R. / Martinez-Ripoll, M. / Garcia, J.L. / Menendez, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v05.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v05.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/2v05 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/2v05 | 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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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: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 6, 2004 / 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: 1.67→21.07 Å / Num. obs: 50379 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.67→76.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.766 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 147 TO 150 AND FROM 169 TO 177, ARE DISORDERED. THEY DO NOT APPEAR IN THE MODEL DISORDERED REGIONS FROM RESIDUES 147 TO 150 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 147 TO 150 AND FROM 169 TO 177, ARE DISORDERED. THEY DO NOT APPEAR IN THE MODEL DISORDERED REGIONS FROM RESIDUES 147 TO 150 AND FROM 169 TO 177. THEY DO NOT APPEAR IN THE MODEL.
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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: 20.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→76.7 Å
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Refine LS restraints |
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