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Yorodumi- PDB-1vk8: CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vk8 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION | ||||||
Components | hypothetical protein TM0486 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI | ||||||
Function / homology | Thiamine-binding protein / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Unknown ligand / Thiamine_BP domain-containing protein Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions. Authors: Dermoun, Z. / Foulon, A. / Miller, M.D. / Harrington, D.J. / Deacon, A.M. / Sebban-Kreuzer, C. / Roche, P. / Lafitte, D. / Bornet, O. / Wilson, I.A. / Dolla, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vk8.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vk8.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 1vk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vk8_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 1vk8_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 1vk8_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1vk8_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/1vk8 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/1vk8 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12423.776 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: protein with possible role in cell wall biogenesis / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0486 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYV6 #2: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #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: 1.97 Å3/Da / Density % sol: 36.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.6 Details: 20% PEG-8000, 0.1M CHES pH 9.5, pH 9.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K. cryo condition: 12% PEG 200. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332, 0.9796 | |||||||||
Detector | Type: ADSC / Detector: CCD / Date: Dec 13, 2003 | |||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→41.71 Å / Num. obs: 25897 / % possible obs: 76.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.97 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.2 | |||||||||
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 607 / Rsym value: 0.116 / % possible all: 23.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→41.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.867 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.142 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, ...Details: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2). AN UNKNOWN LIGAND IS ASSOCIATED WITH EACH OF THE 4 SUBUNITS. UNAMBIGUOUS ASSIGNMENT OF THE IDENTITY OF THIS MOIETY WAS NOT POSSIBLE, THOUGH THE DENSITY CAN BE CLOSELY ACCOUNTED FOR BY A GUANINE BASE. IT IS LABELED 'UNL' AND ALL ATOMS WERE REFINED AS OXYGEN ATOMS. BUMP RESTRAINTS WERE REMOVED FOR THE REFINEMENT OF ATOMS IN EACH OF THESE LIGANDS. 3). TLS GROUPS WERE CHOSEN BY PROTEIN SUBUNIT IDENTIFICATION IN THE CRYSTALLOGRAPHIC ASSYMETRIC UNIT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.411 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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