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- PDB-1g55: Structure of human DNMT2, an enigmatic DNA methyltransferase homologue -

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Basic information

Entry
Database: PDB / ID: 1g55
TitleStructure of human DNMT2, an enigmatic DNA methyltransferase homologue
ComponentsDNA CYTOSINE METHYLTRANSFERASE DNMT2
KeywordsTRANSFERASE / Human DNA Methyltransferase homologue
Function / homology
Function and homology information


tRNA (cytosine38-C5)-methyltransferase / tRNA stabilization / tRNA methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA methylation / tRNA modification / response to amphetamine / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytosine(38)-C(5))-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsDong, A. / Yoder, J.A. / Zhang, X. / Zhou, L. / Bestor, T.H. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
Authors: Dong, A. / Yoder, J.A. / Zhang, X. / Zhou, L. / Bestor, T.H. / Cheng, X.
History
DepositionOct 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA CYTOSINE METHYLTRANSFERASE DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9275
Polymers39,2761
Non-polymers6514
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.5, 116.5, 69.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA CYTOSINE METHYLTRANSFERASE DNMT2


Mass: 39276.371 Da / Num. of mol.: 1 / Mutation: DELETION (RESIDUES 191-237)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O14717, DNA (cytosine-5-)-methyltransferase

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Non-polymers , 5 types, 260 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.3-1.4 M ammonium sulfate, 8 % glycerol, 100 mM glycine-NaOH pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
40.1 %2-mercaptoethanol1drop
5150 mM1dropNaCl
61.3-1.4 Mammonium sulfate1reservoir
78 %glycerol1reservoir
8100 mMglycine-NaOH1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X12C10.98
SYNCHROTRONNSLS X12C20.95189, 0.950051
ROTATING ANODERIGAKU RU20031.54
Detector
TypeIDDetector
BRANDEIS1CCD
RIGAKU RAXIS IV2IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.951891
30.9500511
41.541
ReflectionResolution: 1.8→20 Å / Num. all: 41963 / Num. obs: 146987 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.74 / Num. unique all: 1976 / % possible all: 93.2
Reflection
*PLUS
Num. obs: 41963 / Num. measured all: 146987
Reflection shell
*PLUS
% possible obs: 93.2 % / Num. unique obs: 1976

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.25 1883 5% of total reflection (Random)
Rwork0.21 --
all-37121 -
Displacement parametersBiso mean: 0.943 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 41 256 2771
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d1.5
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_improper_angle_d1.4
LS refinement shellResolution: 1.8→20 Å
RfactorNum. reflection% reflection
Rfree0.25 1883 -
Rwork0.21 --
obs-37121 86 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.2121 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.3748 / Num. reflection obs: 3815 / Rfactor obs: 0.3516

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