+Open data
-Basic information
Entry | Database: PDB / ID: 1yzm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Rabenosyn (458-503), Rab4 binding domain | ||||||
Components | FYVE-finger-containing Rab5 effector protein rabenosyn-5 | ||||||
Keywords | PROTEIN TRANSPORT / Rab Effector / Rabenosyn / Rab GTPase / vesicular trafficking | ||||||
Function / homology | Function and homology information Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / regulation of Golgi organization / early endosome to Golgi transport / endosomal transport / small GTPase binding / Factors involved in megakaryocyte development and platelet production / protein transport / early endosome membrane / endosome ...Toll Like Receptor 9 (TLR9) Cascade / Golgi to lysosome transport / regulation of Golgi organization / early endosome to Golgi transport / endosomal transport / small GTPase binding / Factors involved in megakaryocyte development and platelet production / protein transport / early endosome membrane / endosome / endosome membrane / intracellular membrane-bounded organelle / zinc ion binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yzm.cif.gz | 22.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yzm.ent.gz | 13.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yzm_validation.pdf.gz | 412.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1yzm_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 1yzm_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 1yzm_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzm ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzm | HTTPS FTP |
-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzlC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 1z2aC 1aikS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 5901.560 Da / Num. of mol.: 1 Fragment: RAB4 binding domain, sequence database residues 458-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9H1K0 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.74 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 3, 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: 1.5→50 Å / Num. obs: 7561 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 531 / Rsym value: 0.221 / % possible all: 80.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine-gp41 (PDB ID; 1AIK.pdb) Resolution: 1.5→6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.375 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.817 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.502→1.539 Å / Total num. of bins used: 20
|