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Yorodumi- PDB-2qyh: Crystal structure of the hypothetical protein (gk1056) from geoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qyh | ||||||
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Title | Crystal structure of the hypothetical protein (gk1056) from geobacillus kaustophilus HTA426 | ||||||
Components | Hypothetical conserved protein, GK1056 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Jeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the hypothetical protein (gk1056) from geobacillus kaustophilus HTA426 Authors: Jeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Ebihara, A. / Shinkai, A. / 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 | 2qyh.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qyh.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/2qyh ftp://data.pdbj.org/pub/pdb/validation_reports/qy/2qyh | HTTPS FTP |
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-Related structure data
Related structure data | 2pq0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29898.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL / References: UniProt: Q5L139 #2: Chemical | ChemComp-GOL / #3: 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: 4.94 Å3/Da / Density % sol: 75.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 95mM NaCl, 95mM Hepes pH7.5, 1.52M Ammonium sulfate, 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: 0.97882 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 10, 2006 / Details: RH COATED BENT-CYRINDRICAL MIRROR |
Radiation | Monochromator: SI-1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97882 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 73555 / % possible obs: 99.8 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.081 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.327 / Num. unique all: 7266 / Rsym value: 0.382 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQ0 Resolution: 2.6→25.24 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 891897.47 / 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: 39.7072 Å2 / ksol: 0.331693 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→25.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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