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Yorodumi- PDB-2yzi: Crystal structure of uncharacterized conserved protein from Pyroc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yzi | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Pyrococcus horikoshii | ||||||
Components | Hypothetical protein PH0107 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / sheet/helix/sheet/sheet/helix / Hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized conserved protein from Pyrococcus horikoshii Authors: Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yzi.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzi.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yzi_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 2yzi_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 2yzi_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2yzi_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzi ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15856.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: O57847 #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: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Sodium Chloride, 0.1M Bis-Tris pH 5.5, 25% PEG 3350 , 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: 0.9792, 0.9797, 0.9000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 1, 2006 | ||||||||||||
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→50 Å / Num. obs: 24075 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.018 | ||||||||||||
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.321 / Num. unique all: 2366 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→34.2 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 74736.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.6376 Å2 / ksol: 0.382861 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→34.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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