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Yorodumi- PDB-3hia: Crystal structure of the choline binding domain of Spr1274 in Str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hia | ||||||
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Title | Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae | ||||||
Components | Choline binding protein | ||||||
Keywords | CHOLINE-BINDING PROTEIN / beta hairpin | ||||||
Function / homology | Cholin Binding / left handed beta-beta-3-solenoid / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta / PHOSPHOCHOLINE / Choline binding protein Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Zhang, Z.-Y. / Li, W.-Z. / Jiang, Y.-L. / Bao, R. / Zhou, C.-Z. / Chen, Y.-X. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae Authors: Zhang, Z.-Y. / Li, W.-Z. / Frolet, C. / Bao, R. / Di-guilmi, A.-M. / Jiang, Y.-L. / Zhou, C.-Z. / Chen, Y.-X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hia.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hia.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/3hia ftp://data.pdbj.org/pub/pdb/validation_reports/hi/3hia | HTTPS FTP |
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-Related structure data
Related structure data | 2v05S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10826.836 Da / Num. of mol.: 3 / Fragment: choline binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: spr1274 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DP99 #2: Chemical | ChemComp-PC / #3: Chemical | #4: 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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.75M (NH4)2SO4, 0.1M MES, pH 6.5, 10% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→70.36 Å / Num. obs: 15041 / Redundancy: 3.79 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.26 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.38 / Num. unique all: 2205 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V05 Resolution: 2.38→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.935 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.281 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.538 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.441 Å / Total num. of bins used: 20
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