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Yorodumi- PDB-2x77: Crystal Structure of Leishmania major ADP ribosylation factor-like 1. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x77 | ||||||
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Title | Crystal Structure of Leishmania major ADP ribosylation factor-like 1. | ||||||
Components | ADP-RIBOSYLATION FACTOR | ||||||
Keywords | GTP-BINDING PROTEIN / SMALL GTPASE / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information nuclear lumen / protein targeting to lysosome / ciliary plasm / regulation of endocytosis / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTP binding / Golgi apparatus / cytoplasm Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fleming, J.R. / Dawson, A. / Hunter, W.N. | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2010 Title: Crystal Structure of Leishmania Major Adp Ribosylation Factor-Like 1 and a Classification of Related Gtpase Family Members in This Kinetoplastid. Authors: Fleming, J.R. / Dawson, A. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x77.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x77.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x77_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2x77_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2x77_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2x77_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x77 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x77 | HTTPS FTP |
-Related structure data
Related structure data | 1mozS 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: 21007.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DISULPHIDE LINK BETWEEN C83A AND C83B / Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q4QEJ1 #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: 1.94 Å3/Da / Density % sol: 36.64 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROPS OF 0.75 UL PROTEIN SOLUTION, 0.75 UL 75 MM CALCIUM ACETATE, 17 % PEG 3350. |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98137 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98137 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→78.1 Å / Num. obs: 18516 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MOZ Resolution: 2.1→78.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.817 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 49 TO 54 AND 74 TO 82 IN CHAIN B ARE DISORDERED.
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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: 34.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→78.94 Å
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Refine LS restraints |
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