+Open data
-Basic information
Entry | Database: PDB / ID: 6y7g | ||||||
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Title | Structure of the human RAB3C in complex with GDP | ||||||
Components | Ras-related protein Rab-3C | ||||||
Keywords | STRUCTURAL GENOMICS / RAB3C / human Ras-related protein Rab-3C / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information : / GTP-dependent protein binding / regulation of exocytosis / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / synaptic vesicle ...: / GTP-dependent protein binding / regulation of exocytosis / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / antigen processing and presentation / protein secretion / protein localization to plasma membrane / synaptic vesicle / vesicle / endosome / GTPase activity / GTP binding / perinuclear region of cytoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Diaz-Saez, L. / Jung, S. / Raux, B. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M. / Structural Genomics Consortium (SGC) | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of the human RAB3C in complex with GDP Authors: Diaz-Saez, L. / Jung, S. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Huber, K.V.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y7g.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y7g.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 6y7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y7g_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6y7g_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6y7g_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6y7g_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7g ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7g | HTTPS FTP |
-Related structure data
Related structure data | 1zbdS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25980.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3C / Plasmid: pET28a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96E17 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1M BIS-TRIS pH 6.5 |
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-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→63.78 Å / Num. obs: 16096 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 9.5 / Num. measured all: 57285 / Scaling rejects: 30 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 1ZBD Resolution: 2.3→63.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.867 / SU B: 10.34 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.293 / 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: 99.42 Å2 / Biso mean: 43.127 Å2 / Biso min: 27.52 Å2
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Refinement step | Cycle: final / Resolution: 2.3→63.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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