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Yorodumi- PDB-1weh: Crystal structure of the conserved hypothetical protein TT1887 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1weh | ||||||
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Title | Crystal structure of the conserved hypothetical protein TT1887 from Thermus thermophilus HB8 | ||||||
Components | Conserved hypothetical protein TT1887 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rossmann fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | SLOG cluster4 / SLOG cluster4 family / Rossmann fold - #450 / membrane => GO:0016020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Kukimoto-Niino, M. / Murayama, K. / Idaka, M. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: PROTEIN SCI. / Year: 2004 Title: Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8 Authors: Kukimoto-Niino, M. / Murayama, K. / Kato-Murayama, M. / Idaka, M. / Bessho, Y. / Tatsuguchi, A. / Ushikoshi-Nakayama, R. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1weh.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1weh.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 1weh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1weh_validation.pdf.gz | 366.8 KB | Display | wwPDB validaton report |
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Full document | 1weh_full_validation.pdf.gz | 369 KB | Display | |
Data in XML | 1weh_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1weh_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/1weh ftp://data.pdbj.org/pub/pdb/validation_reports/we/1weh | HTTPS FTP |
-Related structure data
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18578.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLJ9 #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: 2.11 Å3/Da / Density % sol: 41.7 % |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9792, 0.9794, 0.9742 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 20, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 29939 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.87354 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.086 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.268 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2374549.9 / 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: 68.5709 Å2 / ksol: 0.398808 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 15.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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