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- PDB-4fsx: crystal structure of Se-substituted Zea mays ZMET2 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 4fsx
Titlecrystal structure of Se-substituted Zea mays ZMET2 in complex with SAH
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / chromodomain / BAH domain / DNA methyltransferase domain / H3K9me2 binding
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / negative regulation of gene expression via chromosomal CpG island methylation / methylation / chromatin binding / DNA binding / nucleus
Similarity search - Function
Bromo adjacent homology (BAH) domain / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / : / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain ...Bromo adjacent homology (BAH) domain / DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / : / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Vaccinia Virus protein VP39 / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants.
Authors: Du, J. / Zhong, X. / Bernatavichute, Y.V. / Stroud, H. / Feng, S. / Caro, E. / Vashisht, A.A. / Terragni, J. / Chin, H.G. / Tu, A. / Hetzel, J. / Wohlschlegel, J.A. / Pradhan, S. / Patel, D.J. / Jacobsen, S.E.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
B: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,4534
Polymers176,6842
Non-polymers7692
Water00
1
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7272
Polymers88,3421
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7272
Polymers88,3421
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.857, 88.952, 113.493
Angle α, β, γ (deg.)93.47, 95.53, 110.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Chromomethylase 1 / DNA cytosine methyltransferase MET2a / Zea methyltransferase2 / Zmet2


Mass: 88342.172 Da / Num. of mol.: 2 / Fragment: UNP residues 130-912
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: MET2A, ZMET2 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q9AXT8, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 39014 / Num. obs: 38702 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.175 / Rsym value: 0.175 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.595 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→40.25 Å / SU ML: 0.93 / σ(F): 1.35 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 3799 5.01 %
Rwork0.24 --
obs0.241 38685 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.43 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.5146 Å2-1.7924 Å2-0.0951 Å2
2--9.8106 Å2-5.0806 Å2
3---0.704 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10579 0 52 0 10631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310893
X-RAY DIFFRACTIONf_angle_d1.81914780
X-RAY DIFFRACTIONf_dihedral_angle_d20.8964001
X-RAY DIFFRACTIONf_chiral_restr0.1161578
X-RAY DIFFRACTIONf_plane_restr0.0131927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24050.41961130.36762699X-RAY DIFFRACTION97
3.2405-3.28320.37721320.34182630X-RAY DIFFRACTION98
3.2832-3.32810.3321500.32322712X-RAY DIFFRACTION97
3.3281-3.37560.36741060.3012592X-RAY DIFFRACTION97
3.3756-3.4260.33831490.29132741X-RAY DIFFRACTION97
3.426-3.47950.27471280.28892662X-RAY DIFFRACTION98
3.4795-3.53650.28021730.28332587X-RAY DIFFRACTION97
3.5365-3.59750.33571260.27572744X-RAY DIFFRACTION97
3.5975-3.66280.27911370.2742604X-RAY DIFFRACTION97
3.6628-3.73320.28561370.27252634X-RAY DIFFRACTION98
3.7332-3.80940.28591490.24462751X-RAY DIFFRACTION97
3.8094-3.89210.291590.262629X-RAY DIFFRACTION98
3.8921-3.98260.29821460.23692609X-RAY DIFFRACTION97
3.9826-4.08210.24681480.22662685X-RAY DIFFRACTION97
4.0821-4.19240.2571600.21272607X-RAY DIFFRACTION98
4.1924-4.31560.26071270.2082747X-RAY DIFFRACTION98
4.3156-4.45470.28711490.20242644X-RAY DIFFRACTION99
4.4547-4.61370.22341610.18712659X-RAY DIFFRACTION98
4.6137-4.79820.24611340.18712674X-RAY DIFFRACTION98
4.7982-5.01610.21841430.20072744X-RAY DIFFRACTION98
5.0161-5.28010.24691370.20372615X-RAY DIFFRACTION98
5.2801-5.61010.26691270.22932670X-RAY DIFFRACTION98
5.6101-6.04190.24541310.24662703X-RAY DIFFRACTION98
6.0419-6.64750.24531230.25082688X-RAY DIFFRACTION98
6.6475-7.60370.21371330.23492675X-RAY DIFFRACTION98
7.6037-9.55870.21771560.20562675X-RAY DIFFRACTION98
9.5587-40.25160.20741650.24012597X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.85360.57210.53030.68030.32090.887-0.01380.1220.1047-0.0266-0.09320.156-0.0953-0.08220.1181-0.0712-0.0171-0.06970.1781-0.1180.1038-48.403649.5282-56.9939
22.38-0.35610.3030.5491-0.00650.7531-0.0496-0.0968-0.25280.0529-0.0171-0.00120.14310.08610.01320.00370.00690.04720.0741-0.05550.0233-31.096937.8757-53.1576
31.7166-0.02010.38250.69880.10950.97840.0052-0.1211-0.15090.10670.0519-0.04480.18960.07680.06210.06270.0192-0.03270.10040.02770.0809-17.991536.9478-41.9296
41.4696-0.4233-0.24920.49040.27871.0633-0.0982-0.1257-0.25840.0576-0.09460.22030.1997-0.18530.1183-0.17940.01420.14420.2172-0.09170.0498-46.13373.02050.7467
51.62410.2272-0.10850.54510.20840.8015-0.04220.13990.0824-0.11820.1172-0.0969-0.13020.1359-0.0316-0.0579-0.06980.05090.1367-0.0298-0.0639-28.755483.7143-4.0419
60.89980.28490.01340.77520.38050.5542-0.14330.15520.0091-0.28340.1727-0.1329-0.13180.2387-0.0049-0.0756-0.14190.06940.101-0.1212-0.0335-15.799983.3246-14.739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 134:551)
2X-RAY DIFFRACTION2chain 'A' and (resseq 552:685)
3X-RAY DIFFRACTION3chain 'A' and (resseq 686:886)
4X-RAY DIFFRACTION4chain 'B' and (resseq 133:551)
5X-RAY DIFFRACTION5chain 'B' and (resseq 552:685)
6X-RAY DIFFRACTION6chain 'B' and (resseq 686:885)

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