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Yorodumi- PDB-5vn4: Crystal structure of adenine phosphoribosyl transferase from Tryp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vn4 | |||||||||
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Title | Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate | |||||||||
Components | Adenine phosphoribosyltransferase, putative | |||||||||
Keywords | TRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | |||||||||
Function / homology | Function and homology information adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / nucleoside metabolic process / nuclear lumen / glycosome / ciliary plasm / cytoplasm Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Citation | Journal: to be published Title: Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vn4.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vn4.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vn4_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 5vn4_full_validation.pdf.gz | 480.6 KB | Display | |
Data in XML | 5vn4_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 5vn4_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/5vn4 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vn4 | HTTPS FTP |
-Related structure data
Related structure data | 1qb7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 27035.182 Da / Num. of mol.: 2 / Fragment: TrbrA.01405.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote) Strain: 927/4 GUTat10.1 / Gene: Tb927.7.1780 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q57V32, adenine phosphoribosyltransferase #3: Sugar | |
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-Non-polymers , 4 types, 648 molecules
#2: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / | #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: 2.1 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 H10 (289135h10): 25% PEG3350, 100mM HEPES:NaOH, pH 7.5, 5mM AMP, 5mM pyrophosphate, protein conc. 23.85mg/mL, cryo 25% ethylene glycol: unique puck ID: xhs1-4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→50 Å / Num. obs: 100141 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.877 % / Biso Wilson estimate: 13.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Χ2: 1.052 / Net I/σ(I): 20.54 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qb7 Resolution: 1.35→50 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.48 Å2 / Biso mean: 21.1722 Å2 / Biso min: 7.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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