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- PDB-7bv5: Crystal structure of the yeast heterodimeric ADAT2/3 -

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Basic information

Entry
Database: PDB / ID: 7bv5
TitleCrystal structure of the yeast heterodimeric ADAT2/3
Components
  • tRNA-specific adenosine deaminase subunit TAD2
  • tRNA-specific adenosine deaminase subunit TAD3
KeywordsHYDROLASE / deaminase / inosine / auto-inhibition / RNA binding protein / RNA modification
Function / homology
Function and homology information


tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / tRNA-specific adenosine deaminase activity / tRNA modification / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
tRNA-specific adenosine deaminase subunit TAD2 / tRNA-specific adenosine deaminase subunit TAD3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXie, W. / Liu, X. / Chen, R. / Sun, Y. / Chen, R. / Zhou, J. / Tian, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700657 China
CitationJournal: Bmc Biol. / Year: 2020
Title: Crystal structure of the yeast heterodimeric ADAT2/3 deaminase.
Authors: Liu, X. / Chen, R. / Sun, Y. / Chen, R. / Zhou, J. / Tian, Q. / Tao, X. / Zhang, Z. / Luo, G.Z. / Xie, W.
History
DepositionApr 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-specific adenosine deaminase subunit TAD2
B: tRNA-specific adenosine deaminase subunit TAD2
C: tRNA-specific adenosine deaminase subunit TAD3
D: tRNA-specific adenosine deaminase subunit TAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,9178
Polymers132,6564
Non-polymers2624
Water1,946108
1
A: tRNA-specific adenosine deaminase subunit TAD2
C: tRNA-specific adenosine deaminase subunit TAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4594
Polymers66,3282
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-70 kcal/mol
Surface area24660 Å2
MethodPISA
2
B: tRNA-specific adenosine deaminase subunit TAD2
D: tRNA-specific adenosine deaminase subunit TAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4594
Polymers66,3282
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-65 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.591, 118.543, 91.142
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein tRNA-specific adenosine deaminase subunit TAD2 / ATADT2 / tRNA-specific adenosine-34 deaminase subunit TAD2


Mass: 28589.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAD2, YJL035C, J1246 / Production host: Escherichia coli (E. coli) / References: UniProt: P47058, tRNA(adenine34) deaminase
#2: Protein tRNA-specific adenosine deaminase subunit TAD3 / ADAT3 / tRNA-specific adenosine-34 deaminase subunit TAD3


Mass: 37738.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAD3, YLR316C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9URQ3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20-25% PEG 400, 0.1 M MES (pH 6.0-6.5) / PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 37634 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3637 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DH1

3dh1


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.992 / ESU R Free: 0.349
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1889 5 %RANDOM
Rwork0.1999 ---
obs0.2027 37444 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.18 Å2 / Biso mean: 56.2056 Å2 / Biso min: 19.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8097 0 4 108 8209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198260
X-RAY DIFFRACTIONr_bond_other_d0.0010.027549
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9511204
X-RAY DIFFRACTIONr_angle_other_deg3.8583.00117260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85151051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56624.462381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.993151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2651553
X-RAY DIFFRACTIONr_chiral_restr0.0790.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029538
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021895
X-RAY DIFFRACTIONr_mcbond_it3.6285.5894234
X-RAY DIFFRACTIONr_mcbond_other3.6285.5894233
X-RAY DIFFRACTIONr_mcangle_it5.8128.3675275
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 113 -
Rwork0.297 2496 -
all-2609 -
obs--95.22 %

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