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Yorodumi- PDB-2yyv: Crystal structure of uncharacterized conserved protein from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yyv | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Thermotoga maritima | ||||||
Components | Probable 2-phosphosulfolactate phosphatase | ||||||
Keywords | HYDROLASE / Uncharacterized conserved protein / Structural Genomics / 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 / sulfopyruvate decarboxylase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Nakagawa, N. / Nakamura, Y. / Bessho, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized conserved protein from Thermotoga maritima Authors: Nakagawa, N. / Nakamura, Y. / Bessho, Y. / 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 | 2yyv.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yyv.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yyv_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 2yyv_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 2yyv_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2yyv_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyv ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyv | HTTPS FTP |
-Related structure data
Related structure data | 2yzoC 2zbuC 2zbvC 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
#1: Protein | Mass: 24889.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q9WZQ4, 2-phosphosulfolactate phosphatase #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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 10% iso-Propanol, 20% PEG4000, 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: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 13, 2006 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 52400 / % possible obs: 97.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 166159.93 / 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: 39.7342 Å2 / ksol: 0.37434 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→44.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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