- PDB-5ax2: Crystal structure of S.cerevisiae Kti11p -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5ax2
Title
Crystal structure of S.cerevisiae Kti11p
Components
Diphthamide biosynthesis protein 3
Keywords
METAL BINDING PROTEIN / cytoplasm / metal binding / protein folding / high-pressure NMR / MR-SAD
Function / homology
Function and homology information
2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / iron ion binding / zinc ion binding ...2-(3-amino-3-carboxypropyl)histidine synthase activity / oxidoreductase activity, acting on iron-sulfur proteins as donors / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Synthesis of diphthamide-EEF2 / tRNA wobble uridine modification / iron chaperone activity / protein histidyl modification to diphthamide / ferrous iron binding / iron ion binding / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.078 Å / Relative weight: 1
Reflection
Resolution: 2.4→45 Å / Num. obs: 3858 / % possible obs: 95.9 % / Redundancy: 4.9 % / Rsym value: 0.063 / Net I/σ(I): 21.4
Reflection shell
Resolution: 2.4→2.45 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 2.6 / % possible all: 68.6
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.4→45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2617
370
10 %
RANDOM
Rwork
0.23124
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obs
0.2344
3329
95.9 %
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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