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Yorodumi- PDB-2z0j: Crystal structure of uncharacterized conserved protein from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z0j | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8 | ||||||
Components | Putative uncharacterized protein TTHA1438 | ||||||
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 2-phosphosulfolactate phosphatase / 2-phosphosulfolactate phosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Nakagawa, N. / Kukimoto-Niino, M. / 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: Nakagawa, N. / Kukimoto-Niino, M. / 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 | 2z0j.cif.gz | 370.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z0j.ent.gz | 302.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0j ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0j | HTTPS FTP |
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-Related structure data
Related structure data | 2ywaC 2yzyC 2z07C 2z08C 2z09C 2z3vC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24766.414 Da / Num. of mol.: 8 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: Q5SID6 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MES / #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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M MES pH 6.8, 12% PEG 8000, 20% glycerol, 0.16M CaAcetate, 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: BL45XU / Wavelength: 0.9955, 0.9814, 0.9717, 0.9920 | |||||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 27, 2003 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. obs: 320561 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.08 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Rsym value: 0.325 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→45.94 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 715011.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4206 Å2 / ksol: 0.389621 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→45.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
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Xplor file |
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