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- PDB-4lg1: Human Methyltransferase-Like Protein 21D -

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Basic information

Entry
Database: PDB / ID: 4lg1
TitleHuman Methyltransferase-Like Protein 21D
ComponentsProtein-lysine methyltransferase METTL21D
KeywordsTRANSFERASE / Methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptidyl-lysine methylation / peptidyl-lysine trimethylation / negative regulation of ATP-dependent activity / protein-lysine N-methyltransferase activity / histone methyltransferase activity / Protein methylation / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex / cytoplasm / cytosol
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-ADENOSYLMETHIONINE / Protein N-lysine methyltransferase METTL21D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, A. / Zeng, H. / Fenner, M. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Human Methyltransferase-Like Protein 21D in Complex with SAM
Authors: Zeng, H. / Dong, A. / Fenner, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 METTL21D
B: Protein-lysine methyltransferase METTL21D
C: Protein-lysine methyltransferase METTL21D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,01831
Polymers75,6993
Non-polymers1,31928
Water6,521362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.783, 100.052, 96.193
Angle α, β, γ (deg.)90.00, 101.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 149 - 151 / Label seq-ID: 144 - 146

Dom-IDAuth asym-IDLabel asym-ID
1CC
2BB
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Protein-lysine methyltransferase METTL21D / Methyltransferase-like protein 21D / VCP lysine methyltransferase / VCP-KMT


Mass: 25232.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21D, C14orf138 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE-V2R
References: UniProt: Q9H867, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 23 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG 3350, 0.2 M Lithium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 75014 / % possible obs: 91.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.495 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.835.30.78736350.817188.7
1.83-1.865.30.62236670.861190.4
1.86-1.95.40.52936840.886189.1
1.9-1.945.40.4336290.905189.6
1.94-1.985.40.32836620.938188.8
1.98-2.035.40.28336260.977189.1
2.03-2.085.40.2336220.992187.7
2.08-2.135.40.19336371.044189.2
2.13-2.25.40.15335591.078187.7
2.2-2.275.40.13236301.185187.5
2.27-2.355.40.11936121.226188.4
2.35-2.445.40.10336011.278188.5
2.44-2.555.40.08936271.368188.4
2.55-2.695.30.08337341.565190.7
2.69-2.865.30.07338131.846193
2.86-3.085.20.06239682.073196.3
3.08-3.395.20.05440642.594198.4
3.39-3.885.20.04640492.842198.9
3.88-4.885.10.03641132.633199.2
4.88-505.30.03440822.39196.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BZB

3bzb


Resolution: 1.8→33.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.1897 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8437 / SU B: 2.507 / SU ML: 0.078 / SU R Cruickshank DPI: 0.121 / SU Rfree: 0.1145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1529 2 %RANDOM
Rwork0.1957 ---
obs0.1963 74966 91.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.91 Å2 / Biso mean: 28.0726 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-2.7 Å2
2--1.84 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 112 362 5488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195323
X-RAY DIFFRACTIONr_bond_other_d0.0010.025124
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0027219
X-RAY DIFFRACTIONr_angle_other_deg0.734311822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86824.312218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22115944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471528
X-RAY DIFFRACTIONr_chiral_restr0.0760.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021139
X-RAY DIFFRACTIONr_mcbond_it1.6522.6372632
X-RAY DIFFRACTIONr_mcbond_other1.6512.6372632
X-RAY DIFFRACTIONr_mcangle_it2.7183.9373282
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
15LOOSE POSITIONAL0.045
18TIGHT THERMAL14.610.5
15LOOSE THERMAL18.0310
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 94 -
Rwork0.269 5278 -
all-5372 -
obs--88.36 %

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