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Open data
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Basic information
Entry | Database: PDB / ID: 7bvw | ||||||
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Title | Crystal structure of the RING-H2 domain of Arabidopsis RMR1 | ||||||
![]() | AT5G66160 protein | ||||||
![]() | TRANSPORT PROTEIN / C3H2C3 / ring finger / E3 ligase | ||||||
Function / homology | : / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / membrane / AT5G66160 protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chen, S. / Wong, K.B. | ||||||
![]() | ![]() Title: The RING-finger of AtRMR1 (Arabidopsis receptor-homology-transmembrane-RING-H2 sorting receptor 1) is an E3 ligase that mediate its trafficking Authors: Chen, S. / Zeng, Y.L. / Wong, H.Y. / Yang, L. / Luo, F. / Jiang, L.W. / Wong, K.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 57.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v3kS S: Starting model for refinement |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 9220.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.72 Å / Num. obs: 7849 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 9 / Num. measured all: 27884 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.213 / Num. unique obs: 650 / CC1/2: 0.95 / Rpim(I) all: 0.135 / Rrim(I) all: 0.253 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4V3K Resolution: 2.1→32.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.05 Å2 / Biso mean: 27.392 Å2 / Biso min: 12.33 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→32.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 1.4047 Å / Origin y: 5.8871 Å / Origin z: 94.4639 Å
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Refinement TLS group |
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