+Open data
-Basic information
Entry | Database: PDB / ID: 7ezd | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Thorarchaeota Rab co-crystallized with GTP gamma-S | ||||||||||||
Components | Chains: A,B | ||||||||||||
Keywords | SIGNALING PROTEIN / Rab / Small GTPase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||||||||
Authors | Robinson, R.C. / Tran, L.T. | ||||||||||||
Funding support | Japan, United States, 3items
| ||||||||||||
Citation | Journal: To Be Published Title: Structure of Thor-Rab Authors: Robinson, R.C. / Tran, L.T. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ezd.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ezd.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ezd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ezd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ezd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ezd_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 7ezd_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/7ezd ftp://data.pdbj.org/pub/pdb/validation_reports/ez/7ezd | HTTPS FTP |
-Related structure data
Related structure data | 7ezbSC 7ezeC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20887.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea) Gene: AM325_13980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VL07 #2: Chemical | ChemComp-GDP / | #3: Chemical | ChemComp-GSP / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 5.5, 250 mM NaCl, 13% PEG 8000, 5 mM GTP gamma-S |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→44.35 Å / Num. obs: 34996 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.038 / Rrim(I) all: 0.087 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10206 / CC1/2: 0.558 / Rpim(I) all: 0.549 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EZB Resolution: 1.76→44.35 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→44.35 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.76→1.823 Å
|