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- PDB-3lyw: Crystal structure of YbbR family protein Dhaf_0833 from Desulfito... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lyw | ||||||
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Title | Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B | ||||||
![]() | YbbR family protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YbbR family protein Dhaf_0833 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | RNA Polymerase Alpha Subunit; Chain A, domain 2 - #30 / YbbR-like / YbbR-like protein / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Beta Complex / Mainly Beta / YbbR family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B Authors: Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27 KB | Display | ![]() |
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PDB format | ![]() | 20.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
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Full document | ![]() | 422 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10253.337 Da / Num. of mol.: 1 / Fragment: sequence database residues 37-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DCB-2 / DSM 10664 / Gene: Dhaf_0833 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% PEG3350, sodium acetate 10mM, 5% Glycerol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 15491 / Num. obs: 15491 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.7 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.054 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 24 / Num. unique all: 768 / Rsym value: 0.43 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.7502 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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