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- PDB-7cv8: RNA methyltransferase METTL4 -

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Basic information

Entry
Database: PDB / ID: 7cv8
TitleRNA methyltransferase METTL4
ComponentsMethyltransferase-like protein 2
KeywordsNUCLEAR PROTEIN / RNA methyltransferase
Function / homology
Function and homology information


nucleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / nucleic acid binding
Similarity search - Function
MT-A70-like / MT-A70 / MT-A70-like family profile. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsLuo, Q. / Ma, J.
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into molecular mechanism for N6-adenosine methylation by MT-A70 family methyltransferase METTL4
Authors: Luo, Q. / Mo, J. / Chen, H. / Hu, Z. / Wang, B. / Wu, J. / Liang, Z. / Xie, W. / Du, K. / Peng, M. / Li, Y. / Li, T. / Zhang, Y. / Shi, X. / Shen, W.H. / Shi, Y. / Dong, A. / Wang, H. / Ma, J.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 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.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6135
Polymers47,9551
Non-polymers6584
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-1 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.092, 84.404, 93.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methyltransferase-like protein 2


Mass: 47955.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g19340, F18O14.6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8LFA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1M Lithium chloride 0.1M HEPES pH 7.0 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.35→46.96 Å / Num. obs: 17743 / % possible obs: 98.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.054 / Rrim(I) all: 0.188 / Χ2: 1.95 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.438.60.60815960.8830.1950.640.92191.5
2.43-2.53100.52517040.910.160.550.95896.9
2.53-2.6511.40.45817580.9530.1360.4790.9999.4
2.65-2.7912.10.36217590.970.1070.3781.1199.9
2.79-2.96130.30517740.9760.0880.3171.305100
2.96-3.1913.50.24117870.980.0690.2511.633100
3.19-3.5113.10.19617990.9860.0570.2042.131100
3.51-4.0212.40.16318090.9910.0480.172.757100
4.02-5.0612.40.14418170.9920.0430.1513.504100
5.06-3011.50.13919400.9920.0440.1463.40599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.389 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 862 5.2 %RANDOM
Rwork0.1977 ---
obs0.2009 15806 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.86 Å2 / Biso mean: 45.712 Å2 / Biso min: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-25.33 Å20 Å20 Å2
2---12.7 Å2-0 Å2
3----12.63 Å2
Refinement stepCycle: final / Resolution: 2.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 45 61 2892
Biso mean--42.26 39.92 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132908
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172657
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.6543935
X-RAY DIFFRACTIONr_angle_other_deg1.2211.586159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4475331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35322.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74215482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7491517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023171
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02659
LS refinement shellResolution: 2.37→2.428 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.575 40 -
Rwork0.354 839 -
obs--70.49 %
Refinement TLS params.Method: refined / Origin x: 9.0771 Å / Origin y: -13.8904 Å / Origin z: -25.0065 Å
111213212223313233
T0.0389 Å2-0.0234 Å2-0.0048 Å2-0.017 Å2-0.0024 Å2--0.0114 Å2
L0.3716 °20.2067 °20.2821 °2-1.5447 °20.1353 °2--1.0789 °2
S0.0659 Å °-0.0301 Å °-0.0369 Å °-0.097 Å °0.0431 Å °-0.0019 Å °0.0173 Å °0.04 Å °-0.109 Å °

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