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- PDB-5v2n: Crystal Structure of APO Human SETD8 -

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Basic information

Entry
Database: PDB / ID: 5v2n
TitleCrystal Structure of APO Human SETD8
ComponentsN-lysine methyltransferase KMT5A
KeywordsTRANSFERASE / methyl transferase
Function / homology
Function and homology information


histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator ...histone H4K20 monomethyltransferase activity / lysine N-methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / polytene chromosome / peptidyl-lysine monomethylation / protein-lysine N-methyltransferase activity / mitotic chromosome condensation / regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase activity / negative regulation of double-strand break repair via homologous recombination / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / transcription corepressor activity / cell division / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Class V SAM-dependent methyltransferases / : / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. ...Class V SAM-dependent methyltransferases / : / : / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
N-lysine methyltransferase KMT5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSkene, R.J.
CitationJournal: Elife / Year: 2019
Title: The dynamic conformational landscape of the protein methyltransferase SETD8.
Authors: Chen, S. / Wiewiora, R.P. / Meng, F. / Babault, N. / Ma, A. / Yu, W. / Qian, K. / Hu, H. / Zou, H. / Wang, J. / Fan, S. / Blum, G. / Pittella-Silva, F. / Beauchamp, K.A. / Tempel, W. / ...Authors: Chen, S. / Wiewiora, R.P. / Meng, F. / Babault, N. / Ma, A. / Yu, W. / Qian, K. / Hu, H. / Zou, H. / Wang, J. / Fan, S. / Blum, G. / Pittella-Silva, F. / Beauchamp, K.A. / Tempel, W. / Jiang, H. / Chen, K. / Skene, R.J. / Zheng, Y.G. / Brown, P.J. / Jin, J. / Luo, C. / Chodera, J.D. / Luo, M.
History
DepositionMar 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: N-lysine methyltransferase KMT5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6874
Polymers18,5011
Non-polymers1863
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.620, 60.620, 80.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

#1: Protein N-lysine methyltransferase KMT5A / H4-K20-HMTase KMT5A / Histone-lysine N-methyltransferase KMT5A / Lysine N-methyltransferase 5A / ...H4-K20-HMTase KMT5A / Histone-lysine N-methyltransferase KMT5A / Lysine N-methyltransferase 5A / Lysine-specific methylase 5A / PR/SET domain-containing protein 07 / PR/SET07 / SET domain-containing protein 8


Mass: 18500.818 Da / Num. of mol.: 1 / Fragment: UNP residues 231-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT5A, PRSET7, SET07, SET8, SETD8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NQR1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEGMME 550, 5% ethylene glycol, and 100 mM TRIS (pH 8.2-8.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10711 / % possible obs: 99.8 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.04 / Rrim(I) all: 0.135 / Χ2: 1.127 / Net I/σ(I): 6 / Num. measured all: 154975
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2-2.038.90.7340.4020.90697
2.03-2.0710.10.6630.4040.97999.2
2.07-2.1111.10.8260.3430.96999.6
2.11-2.1512.40.8190.3440.973100
2.15-2.214.10.9390.2741.052100
2.2-2.2514.80.9270.2341.0621000.8860.917
2.25-2.3115.80.9530.2331.0281000.9070.937
2.31-2.3715.80.9690.1631.0711000.6330.654
2.37-2.44160.9510.161.0941000.6250.646
2.44-2.5215.90.9710.1371.1441000.5330.551
2.52-2.6115.90.9730.1181.1331000.4610.476
2.61-2.7115.90.9810.0991.2351000.3880.4
2.71-2.8415.90.9860.0831.2251000.3220.332
2.84-2.9915.80.9920.0581.2261000.2250.232
2.99-3.1715.70.9990.0421.2061000.1610.166
3.17-3.4215.70.9980.031.1931000.1160.12
3.42-3.7615.50.9940.0241.2741000.090.094
3.76-4.3115.30.9980.0181.1761000.0690.071
4.31-5.43150.9990.0141.0391000.0530.055
5.43-5013.60.9990.0141.2831000.0480.05

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
HKLdata scaling
RefinementResolution: 2→48.52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2298 / WRfactor Rwork: 0.1631 / FOM work R set: 0.786 / SU B: 11.418 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2073 / SU Rfree: 0.1891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 513 4.8 %RANDOM
Rwork0.1831 ---
obs0.1862 10153 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 41.562 Å2 / Biso min: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2--0.86 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 12 125 1404
Biso mean--50.91 49.3 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191296
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9681734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98323.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6515234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6251511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02972
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 44 -
Rwork0.304 717 -
all-761 -
obs--97.19 %
Refinement TLS params.Method: refined / Origin x: 20.5296 Å / Origin y: 5.0144 Å / Origin z: 18.9415 Å
111213212223313233
T0.1571 Å20.0349 Å2-0.0047 Å2-0.1387 Å2-0.0064 Å2--0.0049 Å2
L0.5799 °2-0.2337 °20.0741 °2-0.477 °20.391 °2--1.6026 °2
S-0.0044 Å °0.0143 Å °-0.0039 Å °-0.0284 Å °-0.067 Å °0.0416 Å °-0.1302 Å °-0.1116 Å °0.0714 Å °

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