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Yorodumi- PDB-3wxi: Crystal structure of trypanosoma brucei gambiense glycerol kinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wxi | ||||||
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Title | Crystal structure of trypanosoma brucei gambiense glycerol kinase (ligand-free form) | ||||||
Components | Glycerol kinase | ||||||
Keywords | TRANSFERASE / GLYCEROL KINASE / TRYPANOSOMA / SUGAR KINASE SUPERFAMILY / Glycosome | ||||||
Function / homology | Function and homology information glycerol kinase / glycerol-3-phosphate biosynthetic process / glycerol kinase activity / glycerol catabolic process / triglyceride metabolic process / phosphorylation / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma brucei gambiense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, T. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, T. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Kita, K. / Harada, S. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2014 Title: Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase. Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, C. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A. / Kita, K. / Harada, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wxi.cif.gz | 202.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wxi.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wxi_validation.pdf.gz | 417.2 KB | Display | wwPDB validaton report |
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Full document | 3wxi_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 3wxi_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 3wxi_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/3wxi ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wxi | HTTPS FTP |
-Related structure data
Related structure data | 3wxjC 3wxkC 3wxlC 2w40S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57064.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote) Gene: gk / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3+pRARE2) / References: UniProt: D3KVM3, glycerol kinase #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: 2.95 Å3/Da / Density % sol: 58.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 26, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 30649 / Num. obs: 29027 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.675 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W40 Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 43.736 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.885 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 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 |
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