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Yorodumi- PDB-3hpd: Structure of hydroxyethylthiazole kinase protein from pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpd | |||||||||
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Title | Structure of hydroxyethylthiazole kinase protein from pyrococcus horikoshii OT3 | |||||||||
Components | Hydroxyethylthiazole kinase | |||||||||
Keywords | TRANSFERASE / ALPHA-BETA / ATP BINDING / KINASE / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Thiamine biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Jeyakanthan, J. / Thamotharan, S. / Kuramitsu, S. / Yokoyama, S. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published Title: Structure of Hydroxyethylthiazole Kinase Protein from Pyrococcus Horikoshii Ot3 Authors: Jeyakanthan, J. / 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 | 3hpd.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpd.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpd ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpd | HTTPS FTP |
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-Related structure data
Related structure data | 1c3qS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28990.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS(DE3)-RIL / References: UniProt: O58877, hydroxyethylthiazole kinase |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % |
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Crystal grow | Temperature: 295 K / Method: microbatch method / pH: 9.3 Details: 0.88M SODIUMCITRATE, 0.1M CHESS, pH 9.3, MICROBATCH METHOD, temperature 295K |
-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 RAXIS / Detector: IMAGE PLATE / Date: Nov 27, 2003 / Details: Mirrors |
Radiation | Monochromator: Si (1 1 1), GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.84 Å / Num. obs: 20162 / % possible obs: 99.8 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.067 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.324 / Num. unique all: 2004 / Rsym value: 0.292 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3Q Resolution: 1.85→19.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 853468.49 / 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: 57.8931 Å2 / ksol: 0.402666 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.1 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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