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- PDB-4qpn: Crystal Structure of Human Methyltransferase-Like Protein 21B -

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Basic information

Entry
Database: PDB / ID: 4qpn
TitleCrystal Structure of Human Methyltransferase-Like Protein 21B
ComponentsProtein-lysine methyltransferase METTL21B
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptidyl-lysine methylation / intracellular anatomical structure / protein-lysine N-methyltransferase activity / heat shock protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / centrosome / protein-containing complex / nucleoplasm / 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 / EEF1A lysine methyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsTempel, W. / Hong, B.S. / Seitova, A. / He, H. / Li, Y. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Human Methyltransferase-Like Protein 21B
Authors: Tempel, W. / Hong, B.S. / Seitova, A. / He, H. / Li, Y. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: 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_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 METTL21B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,57118
Polymers24,9941
Non-polymers57717
Water3,639202
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.665, 38.665, 193.915
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein-lysine methyltransferase METTL21B / Hepatocellular carcinoma-associated antigen 557a / Methyltransferase-like protein 21B


Mass: 24994.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21B, FAM119B, HCA557A / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q96AZ1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.67 Å3/Da / Density % sol: 26.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG-3350, 0.2 M tri-lithium citrate. Protein sample was incubated with SAH overnight. Endopeptidase was added to the protein sample immediately prior to crystallization set up, vapor ...Details: 20% PEG-3350, 0.2 M tri-lithium citrate. Protein sample was incubated with SAH overnight. Endopeptidase was added to the protein sample immediately prior to crystallization set up, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: adsc q315 / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.25→38.78 Å / Num. obs: 45170 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 3 / Num. measured all: 23595 / Num. unique all: 2181 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.5data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: solved with data from isomorphous crystal. model based on pdb entry 4LEC.

4lec


Resolution: 1.25→33.48 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1619 / WRfactor Rwork: 0.1185 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9047 / SU B: 1.482 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0424 / SU Rfree: 0.0449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Structure was solved and model was automatically built (ARP/WARP) using data from a nearly isomorphous crystal. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1667 2190 4.9 %RANDOM
Rwork0.1216 ---
obs0.1238 45060 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.27 Å2 / Biso mean: 12.1595 Å2 / Biso min: 4.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 50 202 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191754
X-RAY DIFFRACTIONr_bond_other_d0.0010.021654
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9672402
X-RAY DIFFRACTIONr_angle_other_deg0.89933802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4323.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30115285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4851515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
X-RAY DIFFRACTIONr_mcbond_it1.5670.973838
X-RAY DIFFRACTIONr_mcbond_other1.5680.974837
X-RAY DIFFRACTIONr_mcangle_it1.991.4761050
X-RAY DIFFRACTIONr_rigid_bond_restr4.62333408
X-RAY DIFFRACTIONr_sphericity_free19.118542
X-RAY DIFFRACTIONr_sphericity_bonded8.00153534
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 181 -
Rwork0.188 3127 -
all-3308 -
obs--99.94 %

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