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Open data
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Basic information
Entry | Database: PDB / ID: 7ezd | ||||||||||||
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Title | Thorarchaeota Rab co-crystallized with GTP gamma-S | ||||||||||||
![]() | Chains: A,B | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Robinson, R.C. / Tran, L.T. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of Thor-Rab Authors: Robinson, R.C. / Tran, L.T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.3 KB | Display | ![]() |
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PDB format | ![]() | 130.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ezbSC ![]() 7ezeC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 20887.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AM325_13980 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-GDP / | ![]() #3: Chemical | ChemComp-GSP / | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7EZB Resolution: 1.76→44.35 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 33.63 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→44.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.823 Å
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