+Open data
-Basic information
Entry | Database: PDB / ID: 4d6v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of signal transducing protein | ||||||
Components | G PROTEIN BETA SUBUNIT GIB2 | ||||||
Keywords | SIGNALING PROTEIN / SCAFFOLD PROTEIN / RIBOSOME BINDING | ||||||
Function / homology | Function and homology information : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | CRYPTOCOCCUS NEOFORMANS VAR. GRUBII H99 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ero, R. / Dimitrova, V.T. / Chen, Y. / Bu, W. / Feng, S. / Liu, T. / Wang, P. / Xue, C. / Tan, S.M. / Gao, Y.G. | ||||||
Citation | Journal: Sci.Rep. / Year: 2015 Title: Crystal Structure of Gib2, a Signal-Transducing Protein Scaffold Associated with Ribosomes in Cryptococcus Neoformans. Authors: Ero, R. / Dimitrova, V.T. / Chen, Y. / Bu, W. / Feng, S. / Liu, T. / Wang, P. / Xue, C. / Tan, S.M. / Gao, Y.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4d6v.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4d6v.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 4d6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d6v_validation.pdf.gz | 427.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4d6v_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 4d6v_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 4d6v_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/4d6v ftp://data.pdbj.org/pub/pdb/validation_reports/d6/4d6v | HTTPS FTP |
-Related structure data
Related structure data | 3frxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34520.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CRYPTOCOCCUS NEOFORMANS VAR. GRUBII H99 (fungus) Strain: H99 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0AUJ0, UniProt: J9W3X8*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE |
---|---|
Crystal grow | Details: 100 MM CACODYLATE,1M SODIUM CITRATE, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 187760 / % possible obs: 99.9 % / Observed criterion σ(I): 2.5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.2→2.35 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FRX Resolution: 2.2→44.016 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 27.55 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→44.016 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|