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Yorodumi- PDB-6gfu: Crystal structure of an ancient sequence-reconstructed Elongation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gfu | |||||||||||||||
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Title | Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262) | |||||||||||||||
Components | Elongation Factor Tu | |||||||||||||||
Keywords | TRANSLATION / Protein synthesis / Elongation Factor / Sequence reconstruction / Ancient protein | |||||||||||||||
Function / homology | Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE Function and homology information | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||
Authors | Majumdar, S. / Tarafder, A.D. / Ge, X. / Kacar, B. / Sanyal, S. | |||||||||||||||
Funding support | Sweden, 4items
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Citation | Journal: To Be Published Title: Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262) Authors: Majumdar, S. / Tarafder, A.D. / Ge, X. / Kacar, B. / Sanyal, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gfu.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gfu.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 6gfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gfu_validation.pdf.gz | 800.4 KB | Display | wwPDB validaton report |
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Full document | 6gfu_full_validation.pdf.gz | 802.7 KB | Display | |
Data in XML | 6gfu_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6gfu_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/6gfu ftp://data.pdbj.org/pub/pdb/validation_reports/gf/6gfu | HTTPS FTP |
-Related structure data
Related structure data | 1efcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44109.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 4000, 20% v/v glycerol 0.03M of each ethylene glycol (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol), 0.1M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→61.85 Å / Num. obs: 33001 / % possible obs: 99.1 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFC Resolution: 2→61.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.288 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.91 Å2 / Biso mean: 35.594 Å2 / Biso min: 21.31 Å2
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Refinement step | Cycle: final / Resolution: 2→61.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.047 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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