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Open data
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Basic information
Entry | Database: PDB / ID: 7cox | ||||||
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Title | Crystal structure of Neisseria meningitidis EarP R268A mutant | ||||||
![]() | Elongation factor P maturation arginine rhamnosyltransferase EarP | ||||||
![]() | TRANSFERASE / Arginine rhamnosyltransferase | ||||||
Function / homology | protein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / translation elongation factor activity / Protein-arginine rhamnosyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H.S. / Yoo, Y. | ||||||
![]() | ![]() Title: Crystal structure of Neisseria meningitidis EarP R268A mutant Authors: Cho, H.S. / Yoo, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.1 KB | Display | ![]() |
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PDB format | ![]() | 129.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.5 KB | Display | ![]() |
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Full document | ![]() | 464.2 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 43987.848 Da / Num. of mol.: 2 / Mutation: E89G, R268A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CNQ34_12095, ERS040961_00525, ERS514851_01386, JY21_02145, NMA510612_1261 Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 3.34 Å3/Da / Density % sol: 63.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium cacodylate pH6.5, 1.26M Ammonium sulfate |
-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: Jul 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.05 Å / Num. obs: 24389 / % possible obs: 99.92 % / Redundancy: 9.7 % / Biso Wilson estimate: 89.97 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1211 / Rpim(I) all: 0.04105 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 3→3.107 Å / Rmerge(I) obs: 1.574 / Num. unique obs: 2372 / CC1/2: 0.623 / CC star: 0.876 / Rpim(I) all: 0.5177 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.05 Å
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Refine LS restraints |
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LS refinement shell |
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