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 / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process ...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 / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / iron ion binding / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function
A: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 B: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 C: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 hetero molecules
A: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 B: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 C: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 hetero molecules
A: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 B: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 C: PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3 hetero molecules
Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Sequence details
FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES A1- A333) AND KTI11 (UNIPROT ID Q3E840, ...FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES A1- A333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES A344-A419) USING A GSGSGSGSGS LINKER (RESIDUES A334-343), LINKER ORDERED FUSION PROTEIN OF KTI13 (UNIPROT ID P31386, RESIDUES B1- B333) AND KTI11 (UNIPROT ID Q3E840, RESIDUES C344-C417) USING A GSGSGSGSGS LINKER (RESIDUES B334,B335,C343), LINKER PARTIALLY ORDERED
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % / Description: NONE
Crystal grow
Details: 100 MM TRIS PH 7.4, 2 M LI2SO4
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626
Detector
Date: Nov 7, 2013
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97626 Å / Relative weight: 1
Reflection
Resolution: 2.9→50 Å / Num. obs: 30909 / % possible obs: 99.4 % / Observed criterion σ(I): 1.5 / Redundancy: 11.06 % / Biso Wilson estimate: 83.79 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.33
Reflection shell
Resolution: 2.9→2.97 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.5 / % possible all: 94.1
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.897→75.635 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 24.17 / Stereochemistry target values: ML Details: KTI13 KTI11 FUSION PROTEIN WITH A GSGSGSGSGSG LINKER. IN CHAIN A THE LINKER IS FULLY VISIBLE, IN CHAINS B AND C THE LINKER IS DISORDERED.
Rfactor
Num. reflection
% reflection
Rfree
0.2188
1546
5 %
Rwork
0.198
-
-
obs
0.1991
30906
99.4 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.897→75.635 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6329
0
17
0
6346
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
6492
X-RAY DIFFRACTION
f_angle_d
0.627
8810
X-RAY DIFFRACTION
f_dihedral_angle_d
11.685
2332
X-RAY DIFFRACTION
f_chiral_restr
0.046
924
X-RAY DIFFRACTION
f_plane_restr
0.004
1173
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8974-2.9909
0.3281
133
0.3143
2531
X-RAY DIFFRACTION
95
2.9909-3.0978
0.3574
141
0.2933
2667
X-RAY DIFFRACTION
100
3.0978-3.2218
0.3169
141
0.2802
2677
X-RAY DIFFRACTION
100
3.2218-3.3684
0.2808
141
0.2622
2695
X-RAY DIFFRACTION
100
3.3684-3.546
0.2603
139
0.235
2631
X-RAY DIFFRACTION
100
3.546-3.7682
0.2596
141
0.2074
2674
X-RAY DIFFRACTION
100
3.7682-4.0591
0.2298
140
0.1877
2671
X-RAY DIFFRACTION
100
4.0591-4.4676
0.1703
141
0.1593
2681
X-RAY DIFFRACTION
100
4.4676-5.1139
0.1681
142
0.1558
2690
X-RAY DIFFRACTION
100
5.1139-6.4425
0.1958
142
0.1836
2690
X-RAY DIFFRACTION
100
6.4425-75.6607
0.2019
145
0.1921
2753
X-RAY DIFFRACTION
100
+
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