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Yorodumi- PDB-3p1w: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p1w | ||||||
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Title | Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c | ||||||
Components | RabGDI protein | ||||||
Keywords | PROTEIN TRANSPORT / GDI RAB / malaria / Structural Genomics Consortium / SGC / transport / PF10_0345 | ||||||
Function / homology | Function and homology information RAB GEFs exchange GTP for GDP on RABs / Rab GDP-dissociation inhibitor activity / small GTPase binding => GO:0031267 / Neutrophil degranulation / small GTPase-mediated signal transduction / vesicle-mediated transport / GTPase activator activity / protein transport / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be published Title: Crystal Structure of RAB GDI from Plasmodium Falciparum, PFL2060c Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / ...Authors: Wernimont, A.K. / Neculai, A.M. / Weadge, J. / MacKenzie, F. / Cossar, D. / Tempel, W. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Langsley, G. / Bosch, J. / Hui, R. / Pizzaro, J.C. / Hutchinson, A. #1: Journal: Mol.Biochem.Parasitol. / Year: 1996 Title: A Plasmodium falciparum homologue of a rab specific GDP dissociation inhibitor. Authors: Attal, G. / Langsley, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p1w.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p1w.ent.gz | 161.1 KB | Display | PDB format |
PDBx/mmJSON format | 3p1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p1w_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 3p1w_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 3p1w_validation.xml.gz | 19 KB | Display | |
Data in CIF | 3p1w_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/3p1w ftp://data.pdbj.org/pub/pdb/validation_reports/p1/3p1w | HTTPS FTP |
-Related structure data
Related structure data | 1lv0S 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: 54353.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL2060c / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I501 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 0.1 M Hepes 7.5, 0.2 M NaCl2, 2 mM TCEP, 5% MPD, glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→50 Å / Num. all: 59119 / Num. obs: 57819 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.038 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 58.69 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LV0 Resolution: 1.85→40.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8908 / SU B: 5.216 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: 43.78 Å2 / Biso mean: 34.569 Å2 / Biso min: 6.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.44 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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Refinement TLS params. | Method: refined / Origin x: 22.4039 Å / Origin y: 14.5863 Å / Origin z: 44.0026 Å
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