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Yorodumi- PDB-2cu5: Crystal Structure Of The Conserved Hypothetical Protein TT1486 Fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cu5 | ||||||
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Title | Crystal Structure Of The Conserved Hypothetical Protein TT1486 From Thermus Thermophilus HB8 | ||||||
Components | Conserved Hypothetical Protein TT1486 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus Thermophilus HB8 / Conserved Hypothetical Protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | YjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Satoh, S. / Nakagawa, N. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Of The Conserved Hypothetical Protein TT1486 From Thermus Thermophilus HB8 Authors: Satoh, S. / Nakagawa, N. / 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 | 2cu5.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cu5.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cu5_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 2cu5_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 2cu5_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2cu5_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cu5 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cu5 | HTTPS FTP |
-Related structure data
Related structure data | 1vmhS S: Starting model for refinement |
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Similar structure data | |
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: 14431.639 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHL7 #2: 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: 1.85 Å3/Da / Density % sol: 32.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: Sodium Chloride, Tris-HCl, Glycerol, pH 7.4, 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: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→44.82 Å / Num. all: 29020 / Num. obs: 29020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.43 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2888 / Rsym value: 0.329 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VMH Resolution: 1.84→41.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1616402.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.3149 Å2 / ksol: 0.374358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.84→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.96 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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