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- PDB-4k25: Crystal Structure of yeast Qri7 homodimer -

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Basic information

Entry
Database: PDB / ID: 4k25
TitleCrystal Structure of yeast Qri7 homodimer
ComponentsProbable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial
KeywordsBIOSYNTHETIC PROTEIN / ASKHA-fold / N6-threonylcarbamoylation enzyme / RNA and metabolite binding / mitochondria
Function / homology
Function and homology information


mitochondrial tRNA threonylcarbamoyladenosine modification / N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / mitochondrion / metal ion binding
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsNeculai, D. / Wan, L. / Mao, D.Y. / Sicheri, F.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system.
Authors: Wan, L.C. / Mao, D.Y. / Neculai, D. / Strecker, J. / Chiovitti, D. / Kurinov, I. / Poda, G. / Thevakumaran, N. / Yuan, F. / Szilard, R.K. / Lissina, E. / Nislow, C. / Caudy, A.A. / Durocher, D. / Sicheri, F.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0953
Polymers42,9901
Non-polymers1052
Water0
1
A: Probable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial
hetero molecules

A: Probable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1906
Polymers85,9792
Non-polymers2114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2420 Å2
ΔGint-95 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.597, 130.983, 47.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two-fold axis: -X, -Y, Z + (1 0 0)

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Components

#1: Protein Probable tRNA threonylcarbamoyladenosine biosynthesis protein QRI7, mitochondrial / t(6)A37 threonylcarbamoyladenosine biosynthesis protein QRI7


Mass: 42989.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: QRI7, YDL104C, D2366 / Production host: Escherichia coli (E. coli) / References: UniProt: P43122
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 8% PEG8000, 0.2M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2011
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.88→20.58 Å / Num. all: 17164 / Num. obs: 9434 / % possible obs: 55 % / Observed criterion σ(F): 2.54 / Observed criterion σ(I): 2.54 / Biso Wilson estimate: 77.86 Å2
Reflection shellResolution: 2.88→2.98 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→20.58 Å / Cor.coef. Fo:Fc: 0.9059 / Cor.coef. Fo:Fc free: 0.8745 / Cross valid method: THROUGHOUT / σ(F): 3.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 947 10.04 %RANDOM
Rwork0.2401 ---
obs0.2456 9434 --
all-17164 --
Displacement parametersBiso mean: 81.54 Å2
Baniso -1Baniso -2Baniso -3
1--8.3918 Å20 Å20 Å2
2--9.4455 Å20 Å2
3----1.0536 Å2
Refine analyzeLuzzati coordinate error obs: 0.625 Å
Refinement stepCycle: LAST / Resolution: 2.88→20.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 2 0 2700
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13725HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d943SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes402HARMONIC5
X-RAY DIFFRACTIONt_it2749HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3010SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.03
X-RAY DIFFRACTIONt_other_torsion20.74
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3186 288 10.89 %
Rwork0.2755 2357 -
all0.2802 2645 -
Refinement TLS params.Method: refined / Origin x: 46.0749 Å / Origin y: 17.508 Å / Origin z: 24.6981 Å
111213212223313233
T0.4964 Å2-0.1017 Å20.1908 Å2-0.1116 Å2-0.1206 Å2--0.0212 Å2
L1.6121 °2-2.7586 °21.3218 °2-7.9538 °2-1.9238 °2--3.4731 °2
S-0.0837 Å °0.1145 Å °-0.134 Å °0.3287 Å °-0.0687 Å °0.2469 Å °-0.2372 Å °0.0716 Å °0.1525 Å °
Refinement TLS groupSelection details: { A|33 - A|602 }

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