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- PDB-5njo: Roll out the beta-barrel: structure and mechanism of Pac13, a uni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5njo | ||||||
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Title | Roll out the beta-barrel: structure and mechanism of Pac13, a unique nucleoside dehydratase | ||||||
![]() | Putative cupin_2 domain-containing isomerase | ||||||
![]() | STRUCTURAL PROTEIN / Pac13 Cupin Pacidamycin | ||||||
Function / homology | RmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / Putative cupin_2 domain-containing isomerase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Michailidou, F. / Bent, A.F. / Naismith, J.H. / Goss, R.J.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins. Authors: Michailidou, F. / Chung, C.W. / Brown, M.J.B. / Bent, A.F. / Naismith, J.H. / Leavens, W.J. / Lynn, S.M. / Sharma, S.V. / Goss, R.J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.2 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.4 KB | Display | ![]() |
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Full document | ![]() | 416.4 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5njnSC ![]() 5oo4C ![]() 5oo5C ![]() 5oo8C ![]() 5oo9C ![]() 5ooaC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 13829.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pac13, pacM / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.1 M Tris pH 8.8, 20% w/v PEG8K, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→57.58 Å / Num. obs: 20630 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 18.63 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.776 / Num. unique obs: 2031 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NJN Resolution: 1.55→57.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.393 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.958 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→57.58 Å
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Refine LS restraints |
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