+Open data
-Basic information
Entry | Database: PDB / ID: 8b5v | ||||||
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Title | Crystal Structure of Trypanosoma Cruzi phosphomannosemutase | ||||||
Components | Phosphomannomutase | ||||||
Keywords | ISOMERASE / TRYPANOSOME GLYCOBIOLOGY | ||||||
Function / homology | Function and homology information phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / hydrolase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Robinson, D.A. / Ferguson, M.A.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Trypanosoma Cruzi phosphomannosemutase Authors: Robinson, D.A. / Ferguson, M.A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b5v.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b5v.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b5v ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b5v | HTTPS FTP |
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-Related structure data
Related structure data | 3f9rS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28271.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053510187.480 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E4A3, phosphomannomutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.29 Å3/Da / Density meas: 46.33 Mg/m3 / Density % sol: 45.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.4 / Details: 0.1M SPG pH 8.4, 24% PEG1500 / PH range: 8.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.55 Å / Num. obs: 63539 / % possible obs: 92.1 % / Redundancy: 4.8 % / CC1/2: 0.976 / Rmerge(I) obs: 0.159 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.663 / Num. unique obs: 2464 / CC1/2: 0.612 / % possible all: 73.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F9R Resolution: 1.6→29.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.154 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 87.15 Å2 / Biso mean: 21.776 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 1.6→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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