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Yorodumi- PDB-2gxf: X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gxf | ||||||
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Title | X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR506. | ||||||
Components | Hypothetical protein yybHHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein YybH Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the Hypothetical Protein YybH from Bacillus subtilis, Northeast Structural Genomics Target SR506 Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / 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 | 2gxf.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gxf.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 2gxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/2gxf ftp://data.pdbj.org/pub/pdb/validation_reports/gx/2gxf | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16408.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: yybH / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P37496 #2: Chemical | ChemComp-MES / #3: 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: 2.46 Å3/Da / Density % sol: 49.94 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15 Details: 100mM MES (pH 6.15), 22% PEG5kMME, 200mM ammonium sulfate, and 5mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904, 0.97943, 0.96801 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006 / Details: mirrors. | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→29.42 Å / Num. all: 22751 / Num. obs: 22660 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.081 / Net I/σ(I): 15.17 | ||||||||||||
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2252 / Rsym value: 0.584 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.1→29.42 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 411496.57 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR phasing.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.266245 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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