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Yorodumi- PDB-2h4o: X-ray Crystal Structure of Protein yonK from Bacillus subtilis. N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h4o | ||||||
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Title | X-ray Crystal Structure of Protein yonK from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR415 | ||||||
Components | YonK protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Bsu2107 (YonK protein) | ||||||
Function / homology | OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #10 / Bacillus phage SPbeta, YonK / YonK superfamily / YonK protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Other non-globular / Special / SPbeta prophage-derived uncharacterized protein YonK Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Seetharaman, J. / Sue, M. / Forouhar, F. / Ken, C. / Bonnie, C. / Ma, L. / Xiao, R. / Acton, T.B. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the hypothetical protein from bacillus subtilis (yonk). Authors: Seetharaman, J. / Sue, M. / Forouhar, F. / Ken, C. / Bonnie, C. / Ma, L. / Xiao, R. / Acton, T.B. / 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 | 2h4o.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h4o.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 2h4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h4o_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 2h4o_full_validation.pdf.gz | 457.7 KB | Display | |
Data in XML | 2h4o_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2h4o_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4o ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4o | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 9012.471 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yonK / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: O31947 #2: 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: 2.26 Å3/Da / Density % sol: 45.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 1000, 100mM TAPS pH 9.0, 120mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913, 0.97941, 0.96780 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2005 / 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: 2.8→50 Å / Num. all: 15558 / Num. obs: 15092 / % possible obs: 0.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: -0.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.046 / Net I/σ(I): 17.7 | ||||||||||||
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 16.1 / Num. unique all: 1704 / Rsym value: 0.181 / % possible all: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→28.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 868587.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.8049 Å2 / ksol: 0.320902 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→28.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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