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- PDB-5wcj: Crystal Structure of Human Methyltransferase-like protein 13 in c... -

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Basic information

Entry
Database: PDB / ID: 5wcj
TitleCrystal Structure of Human Methyltransferase-like protein 13 in complex with SAH
ComponentsMethyltransferase-like protein 13
KeywordsTRANSFERASE / methyltransferase / Rossman fold / SAH-binding / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


negative regulation of cell cycle G1/S phase transition / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Methyltransferase type 11 / Spermine/spermidine synthase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / eEF1A lysine and N-terminal methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHalabelian, L. / Loppnau, P. / Seitova, A. / Hutchinson, A. / Hunt, B. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2018
Title: The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates.
Authors: Jakobsson, M.E. / Malecki, J.M. / Halabelian, L. / Nilges, B.S. / Pinto, R. / Kudithipudi, S. / Munk, S. / Davydova, E. / Zuhairi, F.R. / Arrowsmith, C.H. / Jeltsch, A. / Leidel, S.A. / ...Authors: Jakobsson, M.E. / Malecki, J.M. / Halabelian, L. / Nilges, B.S. / Pinto, R. / Kudithipudi, S. / Munk, S. / Davydova, E. / Zuhairi, F.R. / Arrowsmith, C.H. / Jeltsch, A. / Leidel, S.A. / Olsen, J.V. / Falnes, P.O.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / 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 1.2Oct 4, 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

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Assembly

Deposited unit
A: Methyltransferase-like protein 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9246
Polymers27,5401
Non-polymers3845
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.131, 67.450, 71.230
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 13


Mass: 27539.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL13, KIAA0859, CGI-01 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells
References: UniProt: Q8N6R0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.19 Å3/Da / Density % sol: 43.74 % / Mosaicity: 0.21 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 20% PEG3350, 200mM Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97863 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 26945 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 17.5 / Num. measured all: 172955 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.736.71.05943214120.7190.4351.1391.898.6
9-48.985.50.02812572290.9990.0120.03146.899.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJY

3gjy


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.61 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1288 4.8 %RANDOM
Rwork0.1869 ---
obs0.1882 25607 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.48 Å2 / Biso mean: 35.246 Å2 / Biso min: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å20 Å2
2---1.33 Å20 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 24 62 1722
Biso mean--31.92 39.63 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191738
X-RAY DIFFRACTIONr_bond_other_d0.0010.021651
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.992382
X-RAY DIFFRACTIONr_angle_other_deg0.97833817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87924.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38515271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.874155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211968
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 92 -
Rwork0.302 1873 -
all-1965 -
obs--98.64 %

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