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Yorodumi- PDB-2h6l: X-Ray Crystal Structure of the Metal-containing Protein AF0104 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6l | ||||||
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Title | X-Ray Crystal Structure of the Metal-containing Protein AF0104 from Archaeoglobus fulgidus. Northeast Structural Genomics Consortium Target GR103. | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / X-Ray structure NESG GR103 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Kuzin, A.P. / Abashidze, M. / Fang, Y. / Chen, C. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Kuzin, A.P. / Abashidze, M. / Fang, Y. / Chen, C. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Three dimensional structure of the hypothetical protein AF0104 at the 2.0 A resolution. Authors: Kuzin, A.P. / Abashidze, M. / Fang, Y. / Chen, C. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / 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 | 2h6l.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6l.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h6l_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 2h6l_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 2h6l_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 2h6l_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6l ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6l | 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: 16787.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O30132 #2: Chemical | #3: Chemical | #4: 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: 1.86 Å3/Da / Density % sol: 33.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 40% PEG200, 0.1M Na-acetate, pH 4.6, 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: 0.97925 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 46200 / % possible obs: 94 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 158534.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.9795 Å2 / ksol: 0.401314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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