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Yorodumi- PDB-3guw: Crystal Structure of the TatD-like Protein (AF1765) from Archaeog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3guw | ||||||
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Title | Crystal Structure of the TatD-like Protein (AF1765) from Archaeoglobus fulgidus, Northeast Structural Genomics Consortium Target GR121 | ||||||
Components | uncharacterized protein AF_1765 | ||||||
Keywords | structural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Forouhar, F. / Su, M. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Su, M. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target GR121 Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, 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 | 3guw.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3guw.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 3guw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3guw ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guw | 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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Details | dimer |
-Components
#1: Protein | Mass: 29938.213 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1765 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O28509 #2: Chemical | ChemComp-ZN / |
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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: 2.14 Å3/Da / Density % sol: 42.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M sodium acetate, 1.5M (NH4)2SO4, and 15% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 33352 / Num. obs: 32519 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.07 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.19 / Num. unique all: 3351 / Rsym value: 0.246 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→19.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 484822.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 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: 20.195 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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