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- PDB-6nbj: Qri7 -

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Basic information

Entry
Database: PDB / ID: 6nbj
TitleQri7
Components
  • RNA (5'-R(P*CP*CP*CP*C)-3')
  • tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
KeywordsRNA BINDING PROTEIN / DIMER
Function / homology
Function and homology information


mitochondrial tRNA threonylcarbamoyladenosine modification / N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / nucleotidase activity / tRNA threonylcarbamoyladenosine modification / tRNA binding / mitochondrial matrix / 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
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / RNA / tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å
AuthorsStec, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP.
Authors: Tominaga, T. / Kobayashi, K. / Ishii, R. / Ishitani, R. / Nureki, O.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 0THIS ENTRY 6NBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3WUH, DETERMINED BY T. ...THIS ENTRY 6NBJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3WUH, DETERMINED BY T.TOMINAGA,K.KOBAYASHI,R.ISHII,R.ISHITANI,O.NUREKI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
B: tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
C: RNA (5'-R(P*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,98511
Polymers86,3483
Non-polymers1,6388
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.315, 180.315, 180.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

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Protein / RNA chain , 2 types, 3 molecules ABC

#1: Protein tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial / N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine ...N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine biosynthesis protein QRI7 / tRNA threonylcarbamoyladenosine biosynthesis protein QRI7


Mass: 42585.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: QRI7, YDL104C, D2366 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P43122, N6-L-threonylcarbamoyladenine synthase
#2: RNA chain RNA (5'-R(P*CP*CP*CP*C)-3')


Mass: 1175.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)

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Non-polymers , 7 types, 32 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 400, 3% w/v dextran sulfate sodium salt (Mr 5000), 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→50.1 Å / Num. obs: 22014 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge F all: 0.089 / Net I/σ(I): 8
Reflection shellResolution: 2.94→3.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.94→50.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.988 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26996 1121 5.1 %RANDOM
Rwork0.19633 ---
obs0.20009 20688 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 99.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.94→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 64 98 24 6084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146188
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175608
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6678382
X-RAY DIFFRACTIONr_angle_other_deg0.9071.65313169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6265754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9622.267300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.578151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8511540
X-RAY DIFFRACTIONr_chiral_restr0.0710.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021098
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.08410.1453023
X-RAY DIFFRACTIONr_mcbond_other9.04210.1443021
X-RAY DIFFRACTIONr_mcangle_it13.57615.2023774
X-RAY DIFFRACTIONr_mcangle_other13.57715.2053775
X-RAY DIFFRACTIONr_scbond_it9.93210.6713164
X-RAY DIFFRACTIONr_scbond_other9.88710.6673160
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.52215.8294605
X-RAY DIFFRACTIONr_long_range_B_refined18.781337277
X-RAY DIFFRACTIONr_long_range_B_other18.78307278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.937→3.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 83 -
Rwork0.257 1507 -
obs--99.87 %

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