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Yorodumi- PDB-3cq3: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cq3 | ||||||
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Title | Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (other form) from Thermus Thermophilus HB8 | ||||||
Components | Putative uncharacterized protein TTHB138 | ||||||
Keywords | OXIDOREDUCTASE / Thermus Thermophilus / DTDP-4-Keto-L-Rhamnose Reductase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / 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: 2.1 Å | ||||||
Authors | Jeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (other form) from Thermus Thermophilus HB8 Authors: Jeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kurmamitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cq3.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cq3.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cq3_validation.pdf.gz | 700.6 KB | Display | wwPDB validaton report |
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Full document | 3cq3_full_validation.pdf.gz | 714.4 KB | Display | |
Data in XML | 3cq3_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3cq3_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/3cq3 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/3cq3 | HTTPS FTP |
-Related structure data
Related structure data | 2cu6S 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 11495.020 Da / Num. of mol.: 5 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 |
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-Non-polymers , 5 types, 406 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-P6G / | #5: Chemical | ChemComp-PG4 / | #6: 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: 3.3 Å3/Da / Density % sol: 62.78 % / Description: The file contains friedel pairs |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 18% PEG400, 0.1M Na Acetate, 0.1M Magnesium Chloride , pH4.6, 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: 0.9 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 14, 2004 / Details: RH Coated Bent-Cyrindrical MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 82251 / % possible obs: 99.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.089 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.28 / Rsym value: 0.089 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CU6 Resolution: 2.1→43.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 694419.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The file contains friedel pairs
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.6255 Å2 / ksol: 0.372384 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
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Xplor file |
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