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Yorodumi- PDB-4lbv: Identifying ligand binding hot spots in proteins using brominated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lbv | ||||||
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Title | Identifying ligand binding hot spots in proteins using brominated fragments | ||||||
Components | Elongation factor Tu-A | ||||||
Keywords | PROTEIN BINDING / GTPase | ||||||
Function / homology | Function and homology information translation elongation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å | ||||||
Authors | Groftehauge, M.K. / Therkelsen, M. / Taaning, R. / Skrydstrup, T. / Morth, J.P. / Nissen, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Identifying ligand-binding hot spots in proteins using brominated fragments. Authors: Grftehauge, M.K. / Therkelsen, M.O. / Taaning, R. / Skrydstrup, T. / Morth, J.P. / Nissen, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lbv.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lbv.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/4lbv ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lbv | HTTPS FTP |
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-Related structure data
Related structure data | 4h9gSC 4lbwC 4lbyC 4lbzC 4lc0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44610.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: tuf, tufA / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60338 |
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-Non-polymers , 6 types, 260 molecules
#2: Chemical | ChemComp-GNP / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-NH4 / | ||
#5: Chemical | ChemComp-CL / | ||
#6: Chemical | ChemComp-SO4 / #7: 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: 3.22 Å3/Da / Density % sol: 61.83 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9 Å | ||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 | ||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.02→32.07 Å / Num. obs: 37060 / % possible obs: 97.6 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 1.6 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4H9G Resolution: 2.03→28.081 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.21 / σ(F): 1.38 / Phase error: 19.34 / Stereochemistry target values: ML
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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 max: 101.08 Å2 / Biso mean: 33.1053 Å2 / Biso min: 10.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→28.081 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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