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- PDB-5h6z: Crystal structure of Set7, a novel histone methyltransferase in S... -

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Basic information

Entry
Database: PDB / ID: 5h6z
TitleCrystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe
ComponentsSET domain-containing protein 7
KeywordsTRANSCRIPTION / Histone / methytransferase / Schizosaccharomyces pombe SET7 / Epigenetic
Function / homology
Function and homology information


histone H3K37 methyltransferase activity / sporulation resulting in formation of a cellular spore / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin organization / methylation / chromatin / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase, H3 lysine-37 specific / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain
Similarity search - Domain/homology
AMMONIUM ION / DI(HYDROXYETHYL)ETHER / Histone-lysine N-methyltransferase, H3 lysine-37 specific
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMevius, D.E.H.F. / Shen, Y. / Morishita, M. / Carrozzini, B. / Caliandro, R. / di Luccio, E.
Funding support Korea, Republic Of, Italy, 4items
OrganizationGrant numberCountry
BK21 Plus KNU Creative BioResearch Group, Kyungpook National University Korea, Republic Of
National Research Foundation of Korea (NRF)NRF-2013R1A1A2012486 Korea, Republic Of
NRFCNR-NRF joint projects 2016-2017 #9 Korea, Republic Of
National Research Council (CNR)CNR-NRF joint projects 2016-2017 #9 Italy
CitationJournal: Structure / Year: 2019
Title: Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis.
Authors: Shen, Y. / Mevius, D.E.H.F. / Caliandro, R. / Carrozzini, B. / Roh, Y. / Kim, J. / Kim, S. / Ha, S.C. / Morishita, M. / di Luccio, E.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: SET domain-containing protein 7
B: SET domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,71613
Polymers39,1962
Non-polymers52111
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-54 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.181, 66.181, 257.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-391-

HOH

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Components

#1: Protein SET domain-containing protein 7


Mass: 19597.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: set7, SPCC297.04c / Plasmid: pTYB12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y7Q6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE RESIDUES, A-5-A0, A148-A151, B-5-B0 AND B148-B151 SHOULD BE LABELED AS ...AUTHORS STATE THAT THE RESIDUES, A-5-A0, A148-A151, B-5-B0 AND B148-B151 SHOULD BE LABELED AS 'PTYB12 MULTIPLE CLONING SITE RESIDUE'. THE RESIDUES, A152-A163 AND B152-A163 SHOULD BE LABELED AS 'HUMAN INFLUENZA HEMAGGLUTININ DETECTION TAG'.

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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: 2.08 Å3/Da / Density % sol: 40.81 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5) ...Details: 250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5) Temperature(13), Well volume(500ul), 5uL of HCL (12.1M) was added to the reservoir drop prior to drop setup
Temp details: 13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.999→57.314 Å / Num. obs: 21580 / % possible obs: 91 % / Redundancy: 5.8 % / Net I/σ(I): 4.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.03 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-20002.3.9data reduction
HKL-20002.3.9data scaling
Sir201416.1phasing
PHENIX1.10.1-2155model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMA

3kma


Resolution: 2→57.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.134 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/ F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1111 5.1 %RANDOM
Rwork0.172 ---
obs0.174 20488 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→57.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 29 204 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192083
X-RAY DIFFRACTIONr_bond_other_d0.0020.021916
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9562818
X-RAY DIFFRACTIONr_angle_other_deg1.07434413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5165241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35423.67109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4921516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212330
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1352.82970
X-RAY DIFFRACTIONr_mcbond_other3.1362.818969
X-RAY DIFFRACTIONr_mcangle_it4.8084.2081209
X-RAY DIFFRACTIONr_mcangle_other4.8064.2111210
X-RAY DIFFRACTIONr_scbond_it4.2373.3871113
X-RAY DIFFRACTIONr_scbond_other4.2363.3891114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7224.8871609
X-RAY DIFFRACTIONr_long_range_B_refined9.33423.9412504
X-RAY DIFFRACTIONr_long_range_B_other9.33223.9552505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 59 -
Rwork0.239 1108 -
obs--68.65 %

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