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- PDB-7f4r: Crystal structure of MTA1 -

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Basic information

Entry
Database: PDB / ID: 7f4r
TitleCrystal structure of MTA1
ComponentsMT-a70 family protein
KeywordsDNA BINDING PROTEIN / Protein Complex
Function / homology
Function and homology information


mRNA m6A methyltransferase / mRNA m(6)A methyltransferase activity / RNA N6-methyladenosine methyltransferase complex / methylation / nucleus
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
mRNA m(6)A methyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsChen, J. / Liu, L.
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for MTA1c-mediated DNA N6-adenine methylation
Authors: Chen, J. / Hu, R. / Chen, Y. / Lin, X. / Xiang, W. / Chen, H. / Yao, C. / Liu, L.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: MT-a70 family protein
B: MT-a70 family protein
C: MT-a70 family protein
D: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)92,4544
Polymers92,4544
Non-polymers00
Water9,746541
1
A: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)23,1131
Polymers23,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)23,1131
Polymers23,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)23,1131
Polymers23,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MT-a70 family protein


Theoretical massNumber of molelcules
Total (without water)23,1131
Polymers23,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.872, 112.947, 81.851
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
MT-a70 family protein / MTA1MTase


Mass: 23113.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q22GC0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.15M potassium sodium tartrate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 54422 / % possible obs: 92.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 18.39 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 11.79
Reflection shellResolution: 1.83→1.86 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 3299 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F4O

7f4o


Resolution: 1.83→28.73 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.4044
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 1999 3.67 %
Rwork0.2099 52423 -
obs0.211 54422 76.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.08 Å2
Refinement stepCycle: LAST / Resolution: 1.83→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5719 0 0 541 6260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01385844
X-RAY DIFFRACTIONf_angle_d1.40427873
X-RAY DIFFRACTIONf_chiral_restr0.3128822
X-RAY DIFFRACTIONf_plane_restr0.00641017
X-RAY DIFFRACTIONf_dihedral_angle_d23.63992177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.3215720.27851898X-RAY DIFFRACTION38.85
1.88-1.930.3394870.26172270X-RAY DIFFRACTION46.99
1.93-1.980.31161000.24912618X-RAY DIFFRACTION53.86
1.98-2.050.3251150.2523008X-RAY DIFFRACTION61.24
2.05-2.120.29091260.24463307X-RAY DIFFRACTION68.3
2.12-2.210.28441360.23173576X-RAY DIFFRACTION73.48
2.21-2.310.27191600.22724195X-RAY DIFFRACTION85.98
2.31-2.430.25461700.22974451X-RAY DIFFRACTION91.54
2.43-2.580.26681740.2284564X-RAY DIFFRACTION93.19
2.58-2.780.26861670.23294392X-RAY DIFFRACTION90.08
2.78-3.060.23371680.22994383X-RAY DIFFRACTION89.99
3.06-3.50.231730.20824543X-RAY DIFFRACTION92.47
3.5-4.410.18821710.1654488X-RAY DIFFRACTION91.51
4.41-28.730.19851800.17864730X-RAY DIFFRACTION95.21

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