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- PDB-1w8i: The Structure of gene product af1683 from Archaeoglobus fulgidus. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w8i | ||||||
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Title | The Structure of gene product af1683 from Archaeoglobus fulgidus. | ||||||
![]() | PUTATIVE VAPC RIBONUCLEASE AF_1683 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ARCHAEOGLOBUS FULGIDUS / HYPOTHETICAL PROTEIN / PSI / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Midwest Center for Structural Genomics (MCSG) / Cuff, M.E. / Zhang, R. / Ginell, S.L. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
![]() | ![]() Title: The Structure of Gene Product Af1683 from Archaeoglobus Fulgidus Authors: Cuff, M.E. / Zhang, R. / Ginell, S.L. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.1 KB | Display | ![]() |
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PDB format | ![]() | 33.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.5 KB | Display | ![]() |
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Full document | ![]() | 412.6 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17960.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GENE PRODUCT AF1683 FROM ARCHAEOGLOBUS FULGIDUS / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O28590, Hydrolases; Acting on ester bonds |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62 % |
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Crystal grow | pH: 5.5 / Details: SODIUM CITRATE, PEG 3350, GLYCEROL, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 150 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: CUSTOM- SBC2 / Detector: CCD / Date: Apr 19, 2004 / Details: DUAL SLITS | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. obs: 26396 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.8 | |||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 30.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→57.83 Å
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Refine LS restraints |
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