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- PDB-4lec: Human Methyltransferase-Like Protein 21A -

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Basic information

Entry
Database: PDB / ID: 4lec
TitleHuman Methyltransferase-Like Protein 21A
ComponentsProtein-lysine methyltransferase METTL21A
KeywordsTRANSFERASE / METTL21A / Methyltransferase / Methyltransferase-Like Protein 21A / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptidyl-lysine methylation / protein methyltransferase activity / protein methylation / protein-lysine N-methyltransferase activity / Protein methylation / heat shock protein binding / Hsp70 protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex ...peptidyl-lysine methylation / protein methyltransferase activity / protein methylation / protein-lysine N-methyltransferase activity / Protein methylation / heat shock protein binding / Hsp70 protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex / nucleoplasm / 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-ADENOSYL-L-HOMOCYSTEINE / Protein N-lysine methyltransferase METTL21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDong, A. / Zeng, H. / Fenner, M. / Wernimont, A. / 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 21A in Complex with SAH
Authors: Zeng, H. / Dong, A. / Wu, H.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 METTL21A
B: Protein-lysine methyltransferase METTL21A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53515
Polymers47,7672
Non-polymers76913
Water2,306128
1
A: Protein-lysine methyltransferase METTL21A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2687
Polymers23,8831
Non-polymers3846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein-lysine methyltransferase METTL21A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2688
Polymers23,8831
Non-polymers3847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.166, 72.166, 102.954
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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Components

#1: Protein Protein-lysine methyltransferase METTL21A / Hepatocellular carcinoma-associated antigen 557b / Methyltransferase-like protein 21A


Mass: 23883.275 Da / Num. of mol.: 2 / Fragment: UNP residues 8-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21A, FAM119A, HCA557B / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE-V2R
References: UniProt: Q8WXB1, 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.: 11 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 3350, 0.1 M Succinate Acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 31, 2013 / Details: VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 27200 / Num. obs: 27200 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 45.17 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 19.5
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2 / Num. unique all: 1336 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREP11phasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BZB

2bzb


Resolution: 2.28→36.08 Å / Cor.coef. Fo:Fc: 0.8993 / Cor.coef. Fo:Fc free: 0.8766 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RAMACHANDRAN OUTLIERS AT ACTIVE SITE, A147 TYR, B147 TYR
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 869 3.2 %RANDOM
Rwork0.2188 ---
obs0.22 27162 99.32 %-
Displacement parametersBiso max: 97.75 Å2 / Biso mean: 39.068 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.7499 Å20 Å20 Å2
2---5.7499 Å20 Å2
3---11.4997 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: LAST / Resolution: 2.28→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 63 128 3331
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1140SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes515HARMONIC5
X-RAY DIFFRACTIONt_it3305HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3698SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3305HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4508HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion18.41
LS refinement shellResolution: 2.28→2.37 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3067 94 3.49 %
Rwork0.2573 2597 -
all0.2591 2691 -
obs--99.32 %

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