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- PDB-7eey: The structure of the N-terminal doamin of the Schizosaccharomyces... -

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Basic information

Entry
Database: PDB / ID: 7eey
TitleThe structure of the N-terminal doamin of the Schizosaccharomyces pombe Tad2 adenosine deaminase
ComponentstRNA-specific adenosine deaminase subunit tad2
KeywordsDNA BINDING PROTEIN / Tad2 / tRNA adenosine deaminase
Function / homology
Function and homology information


tRNA-specific adenosine-34 deaminase complex / tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / kinase activity / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
tRNA-specific adenosine deaminase subunit tad2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXie, W. / Liu, X. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Functional and structural investigation of N-terminal domain of the SpTad2/3 heterodimeric tRNA deaminase.
Authors: Liu, X. / Zhou, J. / Ge, R. / Xie, W.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 tad2
D: tRNA-specific adenosine deaminase subunit tad2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80410
Polymers90,2284
Non-polymers5766
Water3,009167
1
B: tRNA-specific adenosine deaminase subunit tad2
C: tRNA-specific adenosine deaminase subunit tad2
hetero molecules

A: tRNA-specific adenosine deaminase subunit tad2
hetero molecules

D: tRNA-specific adenosine deaminase subunit tad2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80410
Polymers90,2284
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_455x-1,y,z1
Buried area7000 Å2
ΔGint-72 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.527, 65.602, 65.642
Angle α, β, γ (deg.)63.974, 69.959, 73.565
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
tRNA-specific adenosine deaminase subunit tad2 / tRNA-specific adenosine-34 deaminase subunit tad2


Mass: 22556.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tad2, SPBC16D10.10 / Production host: Escherichia coli (E. coli) / References: UniProt: O94642, tRNA(adenine34) deaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG2000, 0.1 M NaOAc, 0.2 M (NH4)2SO4

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 26761 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 34.84 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.2
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 15.7 / Num. unique obs: 2603 / CC1/2: 0.986 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UDW

1udw


Resolution: 2.6→34.7 Å / SU ML: 0.2798 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 24.7656 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 1222 4.65 %
Rwork0.1679 25077 -
obs0.1704 26299 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.53 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 30 167 6229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046171
X-RAY DIFFRACTIONf_angle_d0.77488385
X-RAY DIFFRACTIONf_chiral_restr0.0487996
X-RAY DIFFRACTIONf_plane_restr0.00451055
X-RAY DIFFRACTIONf_dihedral_angle_d7.75133771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.3111290.19072712X-RAY DIFFRACTION95.08
2.7-2.820.26451130.1892830X-RAY DIFFRACTION98.36
2.82-2.970.23841100.18772808X-RAY DIFFRACTION98.25
2.97-3.160.25911400.19092789X-RAY DIFFRACTION98.62
3.16-3.40.24621330.17892804X-RAY DIFFRACTION98.59
3.4-3.750.21641400.15882785X-RAY DIFFRACTION98.78
3.75-4.290.22491140.15432847X-RAY DIFFRACTION98.77
4.29-5.40.16681550.14432792X-RAY DIFFRACTION98.63
5.4-34.70.20111880.17522710X-RAY DIFFRACTION97.48

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