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- PDB-4rgk: Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rgk | ||||||
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Title | Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chicago Center for Functional Annotation / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / beta-barrel | ||||||
Function / homology | Gig2-like / Gig2-like / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta / DUF1479 domain-containing protein / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.7 KB | Display | ![]() |
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PDB format | ![]() | 150.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.9 KB | Display | ![]() |
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Full document | ![]() | 464.6 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 47516.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 1.2M monosodium dihydrogen phosphate/0.8 M dipotasium monohydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal monochormator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 25801 / Num. obs: 25801 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.07 Å2 / Rsym value: 0.127 / Net I/σ(I): 9.06 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 1135 / Rsym value: 0.471 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→47.711 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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