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Yorodumi- PDB-5a65: Crystal structure of mouse thiamine triphosphatase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a65 | ||||||
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Title | Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and magnesium ions. | ||||||
Components | THIAMINE TRIPHOSPHATASEThiamine-triphosphatase | ||||||
Keywords | HYDROLASE / TRIPHOSPHATE TUNNEL METALLOENZYME | ||||||
Function / homology | Function and homology information thiamine-triphosphatase / thiamine diphosphate metabolic process / thiamine triphosphate phosphatase activity / Vitamin B1 (thiamin) metabolism / thiamine metabolic process / thiamine diphosphate biosynthetic process / dephosphorylation / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. Authors: Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a65.cif.gz | 175.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a65.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 5a65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a65 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a65 | HTTPS FTP |
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-Related structure data
Related structure data | 5a5yC 5a60C 5a61C 5a64SC 5a66C 5a67C 5a68C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23669.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8JZL3, thiamine-triphosphatase |
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-Non-polymers , 5 types, 137 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #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: 3.28 Å3/Da / Density % sol: 62.55 % / Description: NONE |
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Crystal grow | pH: 9 Details: 27 % PEG 3350,0.2M NACL, 0.1 M TRIS PH 9.0, 0.2M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: May 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→49.4 Å / Num. obs: 44247 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 25.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.66 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 23.85 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A64 Resolution: 1.98→49.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.167 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→49.39 Å
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Refine LS restraints |
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