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- PDB-4d4q: Crystal Structure of Kti13/AtS1 -

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Basic information

Entry
Database: PDB / ID: 4d4q
TitleCrystal Structure of Kti13/AtS1
ComponentsPROTEIN ATS1
KeywordsTRANSLATION / TRNA MODIFICATION / DIPHTHAMIDE MODIFICATION
Function / homology
Function and homology information


tRNA wobble uridine modification / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / cytoplasm
Similarity search - Function
Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.395 Å
AuthorsGlatt, S. / Mueller, C.W.
CitationJournal: Structure / Year: 2015
Title: Structure of the Kti11/Kti13 Heterodimer and its Double Role in Modifications of tRNA and Eukaryotic Elongation Factor 2.
Authors: Glatt, S. / Zabel, R. / Vonkova, I. / Kumar, A. / Netz, D.J. / Pierik, A.J. / Rybin, V. / Lill, R. / Gavin, A. / Balbach, J. / Breunig, K.D. / Muller, C.W.
History
DepositionOct 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ATS1
B: PROTEIN ATS1


Theoretical massNumber of molelcules
Total (without water)73,8332
Polymers73,8332
Non-polymers00
Water724
1
A: PROTEIN ATS1


Theoretical massNumber of molelcules
Total (without water)36,9161
Polymers36,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN ATS1


Theoretical massNumber of molelcules
Total (without water)36,9161
Polymers36,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.750, 96.600, 97.350
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN ATS1 / KTI13 / ALPHA-TUBULIN SUPPRESSOR 1


Mass: 36916.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR RARE / References: UniProt: P31386
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 48.1 % / Description: NONE
Crystal growDetails: 100 MM HEPES PH 7.5 AND 6% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25887 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.33 % / Biso Wilson estimate: 61.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.88
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 8.95 % / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.395→43.302 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 36.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1295 5 %
Rwork0.2341 --
obs0.2355 25852 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.395→43.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4844 0 0 4 4848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025081
X-RAY DIFFRACTIONf_angle_d0.4926898
X-RAY DIFFRACTIONf_dihedral_angle_d11.2421802
X-RAY DIFFRACTIONf_chiral_restr0.036733
X-RAY DIFFRACTIONf_plane_restr0.002915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3951-2.4910.42981400.41152662X-RAY DIFFRACTION99
2.491-2.60430.33691430.35072708X-RAY DIFFRACTION100
2.6043-2.74160.33981460.32282758X-RAY DIFFRACTION100
2.7416-2.91340.39751410.30842683X-RAY DIFFRACTION100
2.9134-3.13820.36571450.29732738X-RAY DIFFRACTION100
3.1382-3.45390.29911440.2732741X-RAY DIFFRACTION100
3.4539-3.95340.24951450.22052755X-RAY DIFFRACTION100
3.9534-4.97970.20191440.19042736X-RAY DIFFRACTION100
4.9797-43.30870.22281470.19332776X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1213-0.3437-2.32065.57442.69496.7639-0.26280.0198-0.46280.16090.00490.21380.6706-0.33520.20440.3573-0.06450.03080.34180.0390.194910.5464-0.145115.9716
22.1378-1.37280.20655.49291.56033.76370.02190.2759-0.2854-0.2546-0.1112-0.4461.3223-0.14170.19890.8801-0.03240.13740.3532-0.07960.410716.7508-7.82230.5711
35.4939-0.83570.74254.67910.63076.7704-0.10231.183-0.4464-1.53560.10430.06450.7462-0.81080.10431.1945-0.27560.11530.6812-0.21790.440710.2701-2.5708-9.2188
42.81860.1091-1.27192.5677-0.63725.8951-0.06860.75420.1386-0.91830.06660.1457-0.3175-0.83940.00350.68080.0801-0.00890.56210.08140.28389.038717.53561.5146
52.9714-0.2641-2.59322.54291.44352.9722-0.4905-0.3815-0.59321.52-0.04850.62391.67770.22810.5611.20390.06950.34970.64620.01580.51663.55428.177942.7495
61.9301-0.56542.08382.9093-0.29722.2959-0.6093-1.0222-0.79660.8066-0.03950.83491.89560.33510.41041.92210.33310.72780.73270.03390.7018-1.57812.142658.902
75.1678-1.44392.30526.9191-2.45923.7239-0.5396-2.5957-0.58761.92810.89840.48121.11610.69580.24281.81080.58150.28741.253-0.05310.48094.428517.530365.5599
86.2592-0.7973-2.19345.62711.91345.513-0.1384-1.18951.23530.46460.82250.009-0.99151.2248-0.32051.5334-0.08870.32240.6758-0.40640.81253.68932.576354.4717
95.6771.7681-1.05553.29021.97412.12430.22311.14670.7162-0.67180.6573-0.0193-1.87790.1698-0.76541.34430.1080.26430.62240.07650.60632.979332.416536.4891
106.35421.9389-2.35732.49742.99798.9189-0.03060.38661.398-0.68830.41750.0869-1.66780.9417-0.24570.79040.12990.08320.41460.09410.5127.813124.233235.1397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 114 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 115 THROUGH 139 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 140 THROUGH 183 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 184 THROUGH 333 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 1 THROUGH 114 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 115 THROUGH 147 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 148 THROUGH 173 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 174 THROUGH 258 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 259 THROUGH 295 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 296 THROUGH 333 )

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