+Open data
-Basic information
Entry | Database: PDB / ID: 7f2a | ||||||
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Title | Crystal structure of Neisseria meningitidis EarP bound TDP | ||||||
Components | Elongation factor P maturation arginine rhamnosyltransferase EarP | ||||||
Keywords | TRANSFERASE / EarP / TDP / Neisseria meningitidis | ||||||
Function / homology | protein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / translation elongation factor activity / THYMIDINE-5'-DIPHOSPHATE / Protein-arginine rhamnosyltransferase Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å | ||||||
Authors | Yoo, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Neisseria meningitidis EarP bound TDP Authors: Yoo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f2a.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f2a.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/7f2a ftp://data.pdbj.org/pub/pdb/validation_reports/f2/7f2a | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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: 44073.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) Gene: earP, CNQ34_12095, ERS040961_00525, ERS514851_01386, H7969_05560, JY21_02145, NMA510612_1261 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5EQ00 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.98 Å |
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: 2.58→45.66 Å / Num. obs: 25556 / % possible obs: 99.88 % / Redundancy: 10.7 % / Biso Wilson estimate: 41.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 23.09 |
Reflection shell | Resolution: 2.58→2.672 Å / Rmerge(I) obs: 0.7574 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 2479 / CC1/2: 0.918 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.58→45.66 Å / SU ML: 0.3714 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2957 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: 42.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→45.66 Å
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Refine LS restraints |
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LS refinement shell |
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