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Yorodumi- PDB-2axp: X-Ray Crystal Structure of Protein BSU20280 from Bacillus subtili... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2axp | ||||||
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Title | X-Ray Crystal Structure of Protein BSU20280 from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR256. | ||||||
Components | hypothetical protein BSU20280 | ||||||
Keywords | UNKNOWN FUNCTION / alpha beta protein. / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information dUDP biosynthetic process / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Forouhar, F. / Abashidze, M. / Friedman, D. / Vorobiev, S.M. / Kuzin, A.P. / Ciao, M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Forouhar, F. / Abashidze, M. / Friedman, D. / Vorobiev, S.M. / Kuzin, A.P. / Ciao, M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Hypothetical Protein BSU20280 from Bacillus subtilis, NESG target SR256 Authors: Forouhar, F. / Abashidze, M. / Friedman, D. / Vorobiev, S.M. / Kuzin, A.P. / Ciao, M. / Conover, K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axp.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axp.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 2axp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2axp_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 2axp_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 2axp_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 2axp_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axp ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axp | 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: 20257.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Species: Bacillus subtilis / Strain: 168 / Gene: yorR / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O31896 #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: 3.8 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium cacodylate (pH 6.5), 17% PEG 8k, 240 mM magnesium acetate, and 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97575 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97575 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 38406 / Num. obs: 38099 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.062 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3718 / Rsym value: 0.281 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 596106.65 / Data cutoff low absF: 0 Isotropic thermal model: OVERALL NCS RESTRAINTS. RMS SIGMA/WEIGHT Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: XtalView was also used for refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.9868 Å2 / ksol: 0.32128 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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