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Yorodumi- PDB-2gsw: Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gsw | ||||||
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Title | Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-Reductase YhdA from Bacillus subtilis, Northeast Structural Genomics Target SR135 | ||||||
Components | yhdA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / FMN binding / oxidoreductase activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.92 Å | ||||||
Authors | Forouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Forouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / 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 Putative NADPH-dependent Azobenzene FMN-Reductase YhdA from Bacillus subtilis, Northeast Structural Genomics Target SR135 Authors: Forouhar, F. / Hussain, M. / Jayaraman, S. / Shen, J. / Cooper, B. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gsw.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gsw.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gsw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2gsw_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2gsw_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 2gsw_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gsw ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gsw | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20278.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Species: Bacillus subtilis / Strain: 168 / Gene: yhdA / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 2633257, UniProt: O07529*PLUS #2: Chemical | ChemComp-FMN / #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: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100mM Tris, 22% PEG3350, 180mM MgCl2, 5 mM NADPH, 5 mM DTT, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97896, 0.97942, 0.96780 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 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: 2.9→29.72 Å / Num. all: 29319 / Num. obs: 28615 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 104.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.072 / Net I/σ(I): 14.3 | ||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.92 / Num. unique all: 2904 / Rsym value: 0.326 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.92→29.72 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 372905.67 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.4155 Å2 / ksol: 0.291943 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.92→29.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.92→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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