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Yorodumi- PDB-3otl: Three-dimensional Structure of the putative uncharacterized prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3otl | ||||||
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Title | Three-dimensional Structure of the putative uncharacterized protein from Rhizobium leguminosarum at the resolution 1.9A, Northeast Structural Genomics Consortium Target RlR261 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | structural genomics / unknown function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein Function and homology information | ||||||
Biological species | Rhizobium leguminosarum bv. viciae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å | ||||||
Authors | Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target RlR261 Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / ...Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3otl.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3otl.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 3otl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/3otl ftp://data.pdbj.org/pub/pdb/validation_reports/ot/3otl | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | dimer,43.24 kD,92.8% |
-Components
#1: Protein | Mass: 17975.709 Da / Num. of mol.: 2 / Mutation: S22A, T30A, S33A, V45Q, P46A, D83N, S97T, A111E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium leguminosarum bv. viciae (bacteria) Strain: 3841 / Gene: RL2761 / References: UniProt: Q1MFM4 #2: Chemical | ChemComp-MES / | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
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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: 2.75 Å3/Da / Density % sol: 55.21 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M NH4Cl, 0.1M MES, 12% PEG 20000, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 60275 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5954 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.901→47.545 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.907 / SU ML: 0.23 / σ(F): 0.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.008 Å2 / ksol: 0.323 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.85 Å2 / Biso mean: 24.788 Å2 / Biso min: 4.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.901→47.545 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: 14
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Refinement TLS params. | Method: refined / Origin x: 41.125 Å / Origin y: 70.3702 Å / Origin z: 44.4942 Å
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Refinement TLS group |
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