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Yorodumi- PDB-3f9r: Crystal Structure of Trypanosoma Brucei phosphomannosemutase, TB.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f9r | ||||||
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Title | Crystal Structure of Trypanosoma Brucei phosphomannosemutase, TB.10.700.370 | ||||||
Components | Phosphomannomutase | ||||||
Keywords | ISOMERASE / trypanosome glycobiology structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information mannose biosynthetic process / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein targeting to ER / glycosome / protein N-linked glycosylation / ciliary plasm / nucleoplasm ...mannose biosynthetic process / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein targeting to ER / glycosome / protein N-linked glycosylation / ciliary plasm / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Wernimont, A.K. / Lam, A. / Ali, A. / Lin, Y.H. / Guther, L. / Shamshad, A. / MacKenzie, F. / Bandini, G. / Kozieradzki, I. / Cossar, D. ...Wernimont, A.K. / Lam, A. / Ali, A. / Lin, Y.H. / Guther, L. / Shamshad, A. / MacKenzie, F. / Bandini, G. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Qiu, W. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Trypanosoma Brucei phosphomannosemutase, TB.10.700.370 Authors: Wernimont, A.K. / Lam, A. / Ali, A. / Lin, Y.H. / Guther, L. / Shamshad, A. / Bandini, G. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / ...Authors: Wernimont, A.K. / Lam, A. / Ali, A. / Lin, Y.H. / Guther, L. / Shamshad, A. / Bandini, G. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Qiu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f9r.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f9r.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 3f9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f9r ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f9r | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27976.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.70.0370, TB10.700.370 / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q38AW2, phosphomannomutase #2: Chemical | #3: Chemical | #4: 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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0 M (NH4)2SO4, 0.2 M NaCl, 0.1 M NaCacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5408 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5408 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 44920 / Num. obs: 44877 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 29.343 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.115 / Χ2: 1.421 / Net I/σ(I): 17.834 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4370 / Rsym value: 0.638 / Χ2: 0.759 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.763 / SU B: 7.576 / SU ML: 0.119 / SU R Cruickshank DPI: 0.169 / SU Rfree: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.167 / 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 max: 64.02 Å2 / Biso mean: 31.63 Å2 / Biso min: 12.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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