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- PDB-7cva: RNA methyltransferase METTL4 -

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Basic information

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


site-specific DNA-methyltransferase (adenine-specific) activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / nucleic acid binding / nucleus
Similarity search - Function
MT-A70 / MT-A70-like / 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
Similarity search - Domain/homology
Methyltransferase-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLuo, Q. / Ma, J.
CitationJournal: To Be Published
Title: Structure of Se-METTL4 at 2.45 Angstromes resolution
Authors: Luo, Q. / Ma, J.
History
DepositionAug 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase-like protein 2
B: Methyltransferase-like protein 2


Theoretical massNumber of molelcules
Total (without water)96,4732
Polymers96,4732
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.812, 94.323, 95.769
Angle α, β, γ (deg.)90.000, 101.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 through 3 and (name N...
21(chain B and (resid 2 through 91 or (resid 92...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 2 through 3 and (name N...A2 - 3
121(chain A and ((resid 2 through 3 and (name N...A2 - 413
131(chain A and ((resid 2 through 3 and (name N...A2 - 413
141(chain A and ((resid 2 through 3 and (name N...A2 - 413
151(chain A and ((resid 2 through 3 and (name N...A2 - 413
211(chain B and (resid 2 through 91 or (resid 92...B2 - 91
221(chain B and (resid 2 through 91 or (resid 92...B92
231(chain B and (resid 2 through 91 or (resid 92...B2 - 414
241(chain B and (resid 2 through 91 or (resid 92...B2 - 414
251(chain B and (resid 2 through 91 or (resid 92...B2 - 414
261(chain B and (resid 2 through 91 or (resid 92...B2 - 414

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Components

#1: Protein Methyltransferase-like protein 2


Mass: 48236.469 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M tacsimate pH 5.5 and 8% PEG3350

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 65279 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.065 / Rrim(I) all: 0.148 / Χ2: 5.404 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.30.41334210.6980.2580.4913.51393.7
2.59-2.693.90.31235650.7690.1720.3591.31797.2
2.69-2.824.10.30135710.7020.1620.3442.05697.6
2.82-2.964.50.22836000.9360.1130.2552.11398.7
2.96-3.154.90.19536420.9640.0940.2172.5999.5
3.15-3.3950.19336350.9290.0960.2164.26598.6
3.39-3.735.60.13936500.9830.0640.1534.65199.4
3.73-4.275.50.11636540.9860.0540.1297.01199.4
4.27-5.385.50.10336780.9880.0490.1149.16599.2
5.38-305.40.10137110.9870.0480.11212.44598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC7.0.076refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.668 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 31.7 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.265 2541 3.89 %
Rwork0.2264 --
obs0.2279 65279 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.49 Å2 / Biso mean: 50.1888 Å2 / Biso min: 10.38 Å2
Refinement stepCycle: final / Resolution: 2.5→29.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 0 11 5337
Biso mean---29.51 -
Num. residues----674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2646X-RAY DIFFRACTION13.468TORSIONAL
12B2646X-RAY DIFFRACTION13.468TORSIONAL
Refinement TLS params.Method: refined / Origin x: -16.4904 Å / Origin y: 0.64 Å / Origin z: -17.2147 Å
111213212223313233
T0.0256 Å20.0117 Å20.0319 Å2-0.0976 Å2-0.006 Å2--0.1009 Å2
L0.1515 °20.0311 °20.1488 °2-0.8611 °2-0.2751 °2--0.7707 °2
S0.0515 Å °0.0219 Å °-0.0174 Å °0.023 Å °-0.0437 Å °-0.0004 Å °-0.0469 Å °0.0555 Å °-0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 413
2X-RAY DIFFRACTION1allB2 - 414
3X-RAY DIFFRACTION1allC1 - 11

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