+Open data
-Basic information
Entry | Database: PDB / ID: 1yzl | ||||||
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Title | GppNHp-Bound Rab9 GTPase | ||||||
Components | Ras-related protein Rab-9A | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab9 / vesicular trafficking | ||||||
Function / homology | Function and homology information RHOBTB3 ATPase cycle / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Rab protein signal transduction / retrograde transport, endosome to Golgi / phagocytic vesicle / cytoplasmic vesicle membrane / phagocytic vesicle membrane / GDP binding ...RHOBTB3 ATPase cycle / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Rab protein signal transduction / retrograde transport, endosome to Golgi / phagocytic vesicle / cytoplasmic vesicle membrane / phagocytic vesicle membrane / GDP binding / melanosome / protein transport / late endosome / lysosome / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzl.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzl.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yzl_validation.pdf.gz | 755.1 KB | Display | wwPDB validaton report |
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Full document | 1yzl_full_validation.pdf.gz | 756.2 KB | Display | |
Data in XML | 1yzl_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1yzl_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzl ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzl | HTTPS FTP |
-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzmC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 1z2aC C: citing same article (ref.) |
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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: 20221.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab9a, Rab9, Sid99 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9R0M6 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: 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: 2.86 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 6000, 200mM Magnesium Chloride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 21, 2003 / Details: osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 19409 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5 / Num. unique all: 19418 / Rsym value: 0.394 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab4 GTPase Resolution: 1.85→4.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.596 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→4.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.854→1.895 Å / Total num. of bins used: 20
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