+Open data
-Basic information
Entry | Database: PDB / ID: 2iwr | ||||||
---|---|---|---|---|---|---|---|
Title | Gtpase Like Domain Of Centaurin Gamma 1 (Human) | ||||||
Components | CENTAURIN GAMMA 1 | ||||||
Keywords | HYDROLASE / ANK REPEAT / ZINC-FINGER / GTP-BINDING / POLYMORPHISM / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / PROTEIN TRANSPORT / GTPASE ACTIVATION / METAL-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION / SGC / ZINC / CENTG1 / GTPASE / ONCOGENE / TRANSPORT / STRUCTUAL GENOMICS CONSORTIUM / STRUCTURAL GENOMICS CONSORTIUM / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport ...Netrin-1 signaling / phosphatidylinositol 3-kinase regulator activity / phosphatidylinositol 3-kinase activator activity / Flemming body / endosomal transport / protein kinase activator activity / positive regulation of protein kinase activity / GTPase activator activity / negative regulation of protein catabolic process / protein transport / actin cytoskeleton organization / negative regulation of neuron apoptotic process / endosome / GTPase activity / GTP binding / protein kinase binding / extracellular exosome / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Elkins, J.M. / Soundararajan, M. / Yang, X. / Papagrigoriou, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Doyle, D.A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Biochem.J. / Year: 2007 Title: The Centaurin Gamma-1 Gtpase-Like Domain Functions as an Ntpase. Authors: Soundararajan, M. / Yang, X. / Elkins, J.M. / Sobott, F. / Doyle, D.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2iwr.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2iwr.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iwr ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iwr | HTTPS FTP |
---|
-Related structure data
Related structure data | 2bmjSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19847.256 Da / Num. of mol.: 1 / Fragment: GTPASE LIKE DOMAIN, RESIDUES 402-577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: IMAGE CONSORTIUM CLONE ID 5218187 / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99490 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.7 % |
---|---|
Crystal grow | pH: 6 / Details: 0.1M PCB PH6.0, 30% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: May 9, 2006 |
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→20.72 Å / Num. obs: 24972 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BMJ Resolution: 1.5→45.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.052 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.084 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.91 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|