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Yorodumi- PDB-2z3v: Crystal structure of uncharacterized conserved protein from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z3v | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 | ||||||
Components | Universal stress protein family | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized conserved protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Iino, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 Authors: Iino, H. / 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 | 2z3v.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z3v.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z3v_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 2z3v_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 2z3v_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2z3v_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z3v ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z3v | HTTPS FTP |
-Related structure data
Related structure data | 2ywaC 2yzyC 2z07C 2z08C 2z09C 2z0jC 1wjgS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14775.985 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJV7 |
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#2: Chemical | ChemComp-PGO / |
#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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 40% v/v 1,2-propanediol, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 11, 2004 |
Radiation | Monochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 19483 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 60.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 9.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WJG Resolution: 1.65→19.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1437087.3 / 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: 76.8562 Å2 / ksol: 0.496626 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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