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- PDB-4mtl: Human Methyltransferase-Like Protein 21C -

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Basic information

Entry
Database: PDB / ID: 4mtl
TitleHuman Methyltransferase-Like Protein 21C
ComponentsProtein-lysine methyltransferase METTL21C
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptidyl-lysine methylation / hormone-mediated apoptotic signaling pathway / protein methylation / protein-lysine N-methyltransferase activity / cellular response to dexamethasone stimulus / skeletal muscle tissue development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / heat shock protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex ...peptidyl-lysine methylation / hormone-mediated apoptotic signaling pathway / protein methylation / protein-lysine N-methyltransferase activity / cellular response to dexamethasone stimulus / skeletal muscle tissue development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / heat shock protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
Lysine methyltransferase / Lysine methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein-lysine methyltransferase METTL21C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsHong, B.S. / Tempel, W. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Methyltransferase-Like Protein 21C
Authors: Hong, B.S. / Tempel, W. / Dong, A. / Li, Y. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Brown, P.J.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Data collection
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-lysine methyltransferase METTL21C
B: Protein-lysine methyltransferase METTL21C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,74941
Polymers54,9802
Non-polymers76939
Water4,378243
1
A: Protein-lysine methyltransferase METTL21C
B: Protein-lysine methyltransferase METTL21C
hetero molecules

A: Protein-lysine methyltransferase METTL21C
B: Protein-lysine methyltransferase METTL21C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,49882
Polymers109,9604
Non-polymers1,53878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7800 Å2
ΔGint-28 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.554, 43.247, 119.454
Angle α, β, γ (deg.)90.000, 99.170, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-1159-

HOH

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Components

#1: Protein Protein-lysine methyltransferase METTL21C / Methyltransferase-like protein 21C


Mass: 27490.059 Da / Num. of mol.: 2 / Fragment: UNP residues 22-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21C, C13orf39 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) V2R-pRARE
References: UniProt: Q5VZV1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 37 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 0.005 M SAH, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→42.09 Å / Num. obs: 62809 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.097 / Mean I/σ(I) obs: 1.2 / Num. measured all: 11457 / Num. unique all: 3048 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.12data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LEC

4lec


Resolution: 1.65→40.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1891 / WRfactor Rwork: 0.1634 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8542 / SU B: 4.051 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0819 / SU Rfree: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE AMINO ACID SEQUENCE OF THE MOLECULAR REPLACEMENT MODEL WAS MODIFIED WITH CHAINSAW. AFTER MOLECULAR REPLACEMENT, PHASES WERE IMPROVED WITH ARP/WARP IN ATOM UPDATE MODE AND WITH DENSITY ...Details: THE AMINO ACID SEQUENCE OF THE MOLECULAR REPLACEMENT MODEL WAS MODIFIED WITH CHAINSAW. AFTER MOLECULAR REPLACEMENT, PHASES WERE IMPROVED WITH ARP/WARP IN ATOM UPDATE MODE AND WITH DENSITY MODIFICATION BY PARROT. AUTOMATIC MODEL BUILDING WAS PERFORMED WITH BUCCANEER, INTERACTIVE MODEL BUILDING WITH COOT, AND GEOMETRY VALIDATION ON THE MOLPROBITY SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1907 3.1 %THIN SHELLS (SFTOOLS)
Rwork0.1691 ---
obs0.1699 62292 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.85 Å2 / Biso mean: 34.4981 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0 Å2-1.83 Å2
2--0.77 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 89 243 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193604
X-RAY DIFFRACTIONr_bond_other_d0.0020.023316
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9764934
X-RAY DIFFRACTIONr_angle_other_deg0.78937648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38525.123162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36215563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.774154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02824
X-RAY DIFFRACTIONr_mcbond_it1.4231.751735
X-RAY DIFFRACTIONr_mcbond_other1.4221.7491734
X-RAY DIFFRACTIONr_mcangle_it1.9962.6192166
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 191 -
Rwork0.29 3975 -
all-4166 -
obs--90.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.06841.23010.8042.5654-0.08132.52760.012-0.6110.10460.0789-0.04890.38050.0314-0.40880.03690.02220.002-0.01340.1173-0.01220.0967-13.03978.861227.8422
20.4470.2872.82542.65884.793621.9218-0.04130.09160.07240.5537-0.2623-0.06630.67920.53040.30360.20040.0435-0.04150.280.01450.07545.50345.8558-7.3354
32.64310.02880.90090.8943-0.11122.66980.02510.2319-0.0371-0.0564-0.0245-0.1024-0.06590.3165-0.00070.0241-0.0092-0.01390.04590.00540.035418.382715.015412.8233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 264
2X-RAY DIFFRACTION2B45 - 57
3X-RAY DIFFRACTION3B58 - 263

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