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Yorodumi- PDB-2cwa: Crystal Structure Of The Single-stranded DNA Binding Protein From... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cwa | ||||||
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Title | Crystal Structure Of The Single-stranded DNA Binding Protein From Thermus Thermophilus HB8 | ||||||
Components | Single-strand binding proteinSingle-strand DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / ssb / single-stranded DNA binding protein / Thermus Thermophilus HB8 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information single-stranded DNA binding / DNA recombination / DNA replication / DNA repair Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å | ||||||
Authors | Satoh, S. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Of The Single-stranded DNA Binding Protein From Thermus Thermophilus HB8 Authors: Satoh, S. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cwa.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cwa.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/2cwa ftp://data.pdbj.org/pub/pdb/validation_reports/cw/2cwa | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30110.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SLP9 | ||
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#2: Chemical | #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: 2.7 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Sodium Nitrate, Tris-HCl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.90000, 0.97905, 0.97940 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2004 | ||||||||||||
Radiation | Monochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.96→39.65 Å / Num. all: 24054 / Num. obs: 24054 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.99 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.3 | ||||||||||||
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2377 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.96→39.65 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2245177.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.9304 Å2 / ksol: 0.40095 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→39.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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