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- PDB-4onq: Crystal structure of ntDRM E283S/R309S/F310S/Y590S/D591S mutant -

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Basic information

Entry
Database: PDB / ID: 4onq
TitleCrystal structure of ntDRM E283S/R309S/F310S/Y590S/D591S mutant
ComponentsDNA methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / DNA methyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / :
Similarity search - Function
SAM-dependent methyltransferase DRM / SAM-dependent methyltransferase DRM-type domain profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / DNA methyltransferase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsDu, J. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Authors: Zhong, X. / Du, J. / Hale, C.J. / Gallego-Bartolome, J. / Feng, S. / Vashisht, A.A. / Chory, J. / Wohlschlegel, J.A. / Patel, D.J. / Jacobsen, S.E.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

Downloads & links

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Assembly

Deposited unit
A: DNA methyltransferase
B: DNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2274
Polymers80,4642
Non-polymers7632
Water2,036113
1
A: DNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6132
Polymers40,2321
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6132
Polymers40,2321
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.504, 131.504, 88.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA methyltransferase / / ntDRM


Mass: 40231.906 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 255-608) / Mutation: E283S/R309S/F310S/Y590S/D591S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: DRM, NtDRM1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q76KU6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium nitrate, 20% PEG3350, 0.1 M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 315 / Detector: CCD / Date: Jul 28, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 31550 / Num. obs: 31550 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 45.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3023 / Rsym value: 0.694 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ONJ

4onj


Resolution: 2.502→32.876 Å / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1524 5.08 %RANDOM
Rwork0.1849 ---
obs0.1872 30026 99.9 %-
all-31550 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→32.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 54 113 5301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155328
X-RAY DIFFRACTIONf_angle_d1.417241
X-RAY DIFFRACTIONf_dihedral_angle_d15.5561981
X-RAY DIFFRACTIONf_chiral_restr0.096786
X-RAY DIFFRACTIONf_plane_restr0.011931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-2.58250.26681360.24182576X-RAY DIFFRACTION99
2.5825-2.67480.33721290.23792605X-RAY DIFFRACTION100
2.6748-2.78180.31451440.23812546X-RAY DIFFRACTION100
2.7818-2.90830.30631350.23482577X-RAY DIFFRACTION100
2.9083-3.06160.25591330.23752609X-RAY DIFFRACTION100
3.0616-3.25320.26431390.21292558X-RAY DIFFRACTION100
3.2532-3.50420.23151480.20352574X-RAY DIFFRACTION100
3.5042-3.85630.28591390.18012616X-RAY DIFFRACTION100
3.8563-4.41320.18041530.15082579X-RAY DIFFRACTION100
4.4132-5.55580.17551400.15222601X-RAY DIFFRACTION100
5.5558-32.87880.22231280.17532661X-RAY DIFFRACTION100
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)
13.6755-0.68771.19531.3323-0.632.1031-0.114-1.01120.07050.5049-0.03670.0924-0.0975-0.48660.15970.6896-0.02980.11750.6505-0.02860.4087-27.796239.78055.89
22.72140.13481.53081.84990.29720.9430.0004-0.53240.37790.1055-0.2090.1815-0.0262-0.34960.17560.53980.00160.16320.3779-0.08190.4691-36.948744.0434-12.2801
35.24261.5494-1.74183.21650.68385.13190.183-0.189-0.0872-0.0261-0.24680.35090.2658-0.72220.04140.3721-0.00340.08110.3515-0.03670.3917-49.538231.7713-21.274
42.99760.55660.86840.84550.12132.25730.01790.05250.01260.1166-0.0349-0.31360.01670.226-0.00270.3792-0.02780.04490.26180.00180.4936-16.561138.6799-11.7718
54.9591.1623-0.80874.569-0.69163.2864-0.1034-0.608-0.62250.8131-0.0533-0.48350.19430.35140.09380.70560.0007-0.10650.52510.12530.5834-7.649133.10262.6524
61.2496-1.05530.34661.318-0.37252.16510.78280.7532-0.3387-1.0156-0.17230.4541-0.05990.0535-0.14111.39580.4847-0.26871.0682-0.32720.6954-30.590272.7885-20.0495
72.3751-0.5138-1.15911.55570.10852.07450.72710.7386-0.0929-0.9065-0.24070.47080.4539-0.51710.29851.0890.2203-0.3080.6181-0.13660.5194-35.951775.0405-7.2639
86.0074-1.89050.76754.80720.99873.8680.21120.5060.0524-0.15430.0880.9259-0.2535-1.2216-0.21870.52340.034-0.17370.72360.14810.6715-53.862681.318510.0834
91.8357-0.9106-0.12672.06071.30622.84530.40330.31270.0297-0.7099-0.1965-0.2953-0.15820.3869-0.13120.69840.1578-0.00240.4266-0.01170.4585-18.504879.2123-2.853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 335 )
2X-RAY DIFFRACTION2chain 'A' and (resid 336 through 382 )
3X-RAY DIFFRACTION3chain 'A' and (resid 383 through 429 )
4X-RAY DIFFRACTION4chain 'A' and (resid 430 through 544 )
5X-RAY DIFFRACTION5chain 'A' and (resid 545 through 604 )
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 289 )
7X-RAY DIFFRACTION7chain 'B' and (resid 290 through 382 )
8X-RAY DIFFRACTION8chain 'B' and (resid 383 through 429 )
9X-RAY DIFFRACTION9chain 'B' and (resid 430 through 603 )

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