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Yorodumi- PDB-2cu6: Crystal Structure Of The dTDP-4-keto-L-rhamnose reductase-related... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cu6 | ||||||
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Title | Crystal Structure Of The dTDP-4-keto-L-rhamnose reductase-related Protein From Thermus Thermophilus HB8 | ||||||
Components | dTDP-4-keto-L-rhamnose reductase-related Protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thermus Thermophilus HB8 / dTDP-4-keto-L-rhamnose reductase-related protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | : / Fe-S cluster assembly (FSCA) / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / MIP18 family-like domain-containing protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Satoh, S. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Of The dTDP-4-keto-L-rhamnose reductase-related Protein From Thermus Thermophilus HB8 Authors: Satoh, S. / 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 | 2cu6.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cu6.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cu6_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
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Full document | 2cu6_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 2cu6_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2cu6_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/2cu6 ftp://data.pdbj.org/pub/pdb/validation_reports/cu/2cu6 | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 11541.915 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W28 #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: 3.56 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Sodium Acetate, PEG 400, Magnesium Chloride, pH 4.0, 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: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20442 / Num. obs: 20442 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 9 / Num. unique all: 2026 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.16 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3387823.06 / 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: 45.9527 Å2 / ksol: 0.378654 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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