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- PDB-6a5k: Crystal structure of Arabidopsis thaliana SUVH6 in complex with S... -

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Basic information

Entry
Database: PDB / ID: 6a5k
TitleCrystal structure of Arabidopsis thaliana SUVH6 in complex with SAM, form 1
ComponentsHistone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6Histone methyltransferase
KeywordsGENE REGULATION / SRA / SET / histone methyltransferase / DNA methylation
Function / homology
Function and homology information


methyl-CpNpG binding / methyl-CpNpN binding / : / [histone H3]-lysine9 N-methyltransferase / histone H3K9me2 methyltransferase activity / methyl-CpG binding / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / zinc ion binding / nucleus
Similarity search - Function
Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. ...Histone H3-K9 methyltransferase, plant / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / PUA-like superfamily / 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
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLi, X. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Authors: Li, X. / Harris, C.J. / Zhong, Z. / Chen, W. / Liu, R. / Jia, B. / Wang, Z. / Li, S. / Jacobsen, S.E. / Du, J.
History
DepositionJun 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0976
Polymers59,4371
Non-polymers6605
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.113, 122.152, 56.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 / Histone methyltransferase / Histone H3-K9 methyltransferase 6 / H3-K9-HMTase 6 / Protein SET DOMAIN GROUP 23 / Suppressor of ...Histone H3-K9 methyltransferase 6 / H3-K9-HMTase 6 / Protein SET DOMAIN GROUP 23 / Suppressor of variegation 3-9 homolog protein 6 / Su(var)3-9 homolog protein 6


Mass: 59437.230 Da / Num. of mol.: 1 / Mutation: P777L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUVH6, SDG23, SET23, At2g22740, T9I22.18 / Plasmid: pET-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q8VZ17, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M potassium sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2827 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 42734 / % possible obs: 99.9 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 41.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2102 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.878 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.214 2098 5.04 %
Rwork0.1841 --
obs0.1856 41533 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 31 403 4115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053780
X-RAY DIFFRACTIONf_angle_d0.9455091
X-RAY DIFFRACTIONf_dihedral_angle_d15.4191439
X-RAY DIFFRACTIONf_chiral_restr0.038547
X-RAY DIFFRACTIONf_plane_restr0.003657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92320.2937840.24561834X-RAY DIFFRACTION66
1.9232-1.94750.32061020.23932223X-RAY DIFFRACTION80
1.9475-1.97310.26351350.22742382X-RAY DIFFRACTION88
1.9731-2.00020.21871360.21482655X-RAY DIFFRACTION96
2.0002-2.02880.25841370.21712790X-RAY DIFFRACTION99
2.0288-2.0590.24931440.20542697X-RAY DIFFRACTION100
2.059-2.09120.25631530.20192763X-RAY DIFFRACTION100
2.0912-2.12550.22341520.19592720X-RAY DIFFRACTION100
2.1255-2.16210.22391390.1912791X-RAY DIFFRACTION100
2.1621-2.20150.18911700.19232691X-RAY DIFFRACTION100
2.2015-2.24380.23731460.18712770X-RAY DIFFRACTION100
2.2438-2.28960.24161340.20192711X-RAY DIFFRACTION100
2.2896-2.33940.26521420.18992769X-RAY DIFFRACTION100
2.3394-2.39380.19491200.19382759X-RAY DIFFRACTION100
2.3938-2.45370.27181480.18992764X-RAY DIFFRACTION100
2.4537-2.520.22631700.17782671X-RAY DIFFRACTION100
2.52-2.59420.21561670.1932730X-RAY DIFFRACTION100
2.5942-2.67790.2231360.17622795X-RAY DIFFRACTION100
2.6779-2.77360.20731420.18222736X-RAY DIFFRACTION100
2.7736-2.88460.21721340.18412730X-RAY DIFFRACTION100
2.8846-3.01590.19121530.18212750X-RAY DIFFRACTION100
3.0159-3.17490.19061710.17772735X-RAY DIFFRACTION100
3.1749-3.37370.20871520.16662727X-RAY DIFFRACTION100
3.3737-3.63410.18181260.16032747X-RAY DIFFRACTION100
3.6341-3.99970.18261250.15772802X-RAY DIFFRACTION100
3.9997-4.5780.17751610.14992711X-RAY DIFFRACTION100
4.578-5.76630.19031500.18572736X-RAY DIFFRACTION100
5.7663-47.8930.25281470.21982717X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2795-0.370.66221.23660.16831.724-0.09120.54580.2666-0.2202-0.041-0.2082-0.13110.28880.10820.19490.02760.01330.23720.06510.135338.549343.799927.8461
22.3-1.00580.54041.2159-0.34470.98190.11440.3338-0.052-0.2646-0.13370.2635-0.04340.05680.01610.22190.0558-0.05050.1513-0.03390.188516.952544.202325.0745
32.1004-0.90850.67971.0995-0.75431.37130.0577-0.0368-0.0323-0.05340.04990.1598-0.1182-0.14590.02260.15350.0534-0.02110.0954-0.03080.209810.443550.372531.3278
42.73190.6422-0.16411.0657-0.16781.38370.0366-0.91661.01310.7758-0.18150.2153-0.62-0.50220.03130.31150.20220.00670.4067-0.29390.204826.110348.88163.4149
52.7506-1.2257-0.2421.27530.23990.0597-0.4006-0.81090.73240.62850.1555-0.2065-0.29750.48840.4410.2496-0.2583-0.13420.1720.12830.497256.593248.236854.497
61.3407-0.05990.93041.4277-0.16251.3456-0.1484-0.07220.41880.0432-0.1226-0.3155-0.24640.12320.03770.13820.0036-0.05350.07360.01270.18442.875447.132447.1443
71.704-0.67840.46150.942-0.16342.3891-0.0438-0.1468-0.13430.0298-0.0004-0.06570.1425-0.10760.11310.1356-0.0151-0.00550.21230.01540.177844.758131.781153.7829
81.1097-0.1867-0.06450.9546-0.45730.9295-0.1559-0.41010.05340.1213-0.0559-0.2486-0.2411-0.00790.11540.14620.019-0.03460.1699-0.00840.069740.872939.462354.421
92.05960.37110.04770.7217-0.25861.1178-0.0305-0.2839-0.22860.0623-0.0815-0.12030.0726-0.09890.02430.11580.00670.01630.13820.01670.109733.969732.07451.5507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 267 through 317 )
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 418 )
3X-RAY DIFFRACTION3chain 'A' and (resid 419 through 498 )
4X-RAY DIFFRACTION4chain 'A' and (resid 499 through 537 )
5X-RAY DIFFRACTION5chain 'A' and (resid 538 through 560 )
6X-RAY DIFFRACTION6chain 'A' and (resid 561 through 647 )
7X-RAY DIFFRACTION7chain 'A' and (resid 648 through 705 )
8X-RAY DIFFRACTION8chain 'A' and (resid 706 through 735 )
9X-RAY DIFFRACTION9chain 'A' and (resid 736 through 790 )

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