- PDB-5tu6: PagF prenyltransferase with cyclic[INPYLYP] and DMSPP -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5tu6
Title
PagF prenyltransferase with cyclic[INPYLYP] and DMSPP
Components
PagF prenyltransferase
cyclic[INPYLYP] peptide
Keywords
TRANSFERASE / RiPP / prenylation / ABBA fold
Function / homology
Peptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / metal ion binding / DIMETHYLALLYL S-THIOLODIPHOSPHATE / METHIONINE / Putative prenyl transferase
Type: MARRESEARCH / Detector: CCD / Date: Aug 19, 2014
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97856 Å / Relative weight: 1
Reflection
Resolution: 2.22→50 Å / Num. obs: 116928 / % possible obs: 93.5 % / Redundancy: 3.7 % / Rsym value: 0.91 / Net I/σ(I): 12.7
Reflection shell
Resolution: 2.2→2.3 Å / Rsym value: 0.673
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0151
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.723 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.221 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23945
844
5 %
RANDOM
Rwork
0.18144
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obs
0.18434
16035
99.55 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å