+Open data
-Basic information
Entry | Database: PDB / ID: 1yoz | ||||||
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Title | Predicted coding region AF0941 from Archaeoglobus fulgidus | ||||||
Components | Hypothetical protein AF0941 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF0941 / APC5573 / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PROTEIN STRUCTURE INITIATIVE / PSI | ||||||
Function / homology | AF0941-like / Uncharacterised domain AF0941 / AF0941-like superfamily / AF0941-like / Hypothetical protein af0941 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein AF_0941 Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Lunin, V.V. / Zhang, R. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of predicted coding region AF0941 from Archaeoglobus fulgidus Authors: Lunin, V.V. / Botchkareva, E. / Zhang, R. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yoz.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yoz.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yoz_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 1yoz_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 1yoz_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1yoz_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yoz ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yoz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13789.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: MODIFIED PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O29321 #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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.5M (NH4)2SO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.97946 / Wavelength: 0.97946 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63 Å / Num. all: 17895 / Num. obs: 17895 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.049 / Net I/σ(I): 56.67 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 8.1 / Rsym value: 0.383 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→62.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.723 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.995 Å2
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Refinement step | Cycle: LAST / Resolution: 2→62.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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