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- PDB-3qv2: Structure Analysis of Entamoeba histolytica methyltransferase EhMeth -

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Basic information

Entry
Database: PDB / ID: 3qv2
TitleStructure Analysis of Entamoeba histolytica methyltransferase EhMeth
Components5-cytosine DNA methyltransferase
KeywordsTRANSFERASE / Methyltransferase / DNMT2 / EhMeth
Function / homology
Function and homology information


tRNA (cytidine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / sporulation resulting in formation of a cellular spore / nucleus
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / 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
S-ADENOSYL-L-HOMOCYSTEINE / 5-cytosine DNA methyltransferase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSchulz, E.C. / Roth, H.M. / Ankri, S. / Ficner, R.
CitationJournal: To be Published
Title: Crystal Structure Analysis of Entamoeba histolytica Methyltransferase
Authors: Schulz, E.C. / Roth, H.M. / Ankri, S. / Ficner, R.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 5-cytosine DNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5475
Polymers37,8741
Non-polymers6734
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.970, 46.970, 303.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 5-cytosine DNA methyltransferase / DNA (Cytosine-5)-methyltransferase


Mass: 37874.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: meth, EHI_069140 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6Q386, DNA (cytosine-5-)-methyltransferase
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M MES, 22% PEG 8000 (w/v), 0.2 M (NH4)2SO4, pH 6,5, vapor diffusion, temperature 298K
PH range: 6,5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.981 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 19536 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.99
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.20.5152.46199.9
2.2-2.30.4382.9199.6
2.3-2.50.3123.91199.7
2.5-3.320.1278.65199.6
3.32-3.730.05618.19198.9
3.73-4.140.04322.98199.2
4.14-4.550.03625.97198.7
4.55-140.03426.62196.4
14-170.01937.69181.6
17-500.03135.12183.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46.416 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.25 / σ(F): 0 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1098 5.93 %
Rwork0.2183 --
obs0.2212 18527 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.534 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4122 Å20 Å2-0 Å2
2--4.4122 Å20 Å2
3----6.283 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 41 224 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022720
X-RAY DIFFRACTIONf_angle_d0.6143680
X-RAY DIFFRACTIONf_dihedral_angle_d16.5171058
X-RAY DIFFRACTIONf_chiral_restr0.045404
X-RAY DIFFRACTIONf_plane_restr0.002467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.24790.33541130.28011940X-RAY DIFFRACTION86
2.2479-2.36640.34291300.27282030X-RAY DIFFRACTION90
2.3664-2.51460.31221310.26022064X-RAY DIFFRACTION92
2.5146-2.70880.28031350.24892146X-RAY DIFFRACTION95
2.7088-2.98130.26191400.22762225X-RAY DIFFRACTION97
2.9813-3.41260.31541450.21922260X-RAY DIFFRACTION98
3.4126-4.29910.21031470.18432319X-RAY DIFFRACTION98
4.2991-46.42730.23371570.18652445X-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)
10.00720.00260.00280.0059-0.00370.01020.0059-0.00110.01540.0001-0.00470.0099-0.0298-0.016-0.00520.15730.09480.0928-0.0611-0.0057-0.07626.7963-17.446629.0402
20.02190.0147-0.0020.0106-0.0036-0.00020.0253-0.03370.01610.00250.0164-0.0328-0.03470.0273-0.01540.1461-0.08240.025-0.02570.1006-0.077120.236-19.018929.4757
30.0207-0.0123-0.02390.04030.03760.0415-0.00610.025-0.02310.0045-0.03610.0003-0.0565-0.00150.03270.12490.07250.02340.0577-0.00950.057116.6621-32.971218.7314
40.058-0.0538-0.05120.09950.03760.04580.05780.0157-0.0527-0.07490.0189-0.0298-0.0259-0.0209-0.02780.10480.0614-0.038-0.07210.10540.00196.0195-32.15923.4349
50.01110.00280.03920.00070.00890.1348-0.0049-0.01640.0111-0.00710.01050.00590.0015-0.07880.00060.3480.17750.10380.24510.05370.1181-3.7204-12.042511.3288
60.00510.0072-0.00310.02210.00730.0190.01980.00110.01230.00110.01230.0125-0.0481-0.0238-0.01280.33720.1220.10460.1010.01360.063411.969-8.7657-4.2641
70.00960.0033-0.01850.01670.00660.04540.02930.0092-0.0161-0.0193-0.0105-0.0039-0.0348-0.0256-0.01280.18250.11070.03350.05370.09410.027512.1662-13.84020.3907
80.1219-0.0891-0.1370.0650.10020.1542-0.0022-0.0005-0.0050.01650.03570.0037-0.0006-0.0051-0.03070.37830.2343-0.13940.5456-0.05660.30890.6094-9.8852-8.9787
90.36810.00830.0692.5238-1.4810.8839-0.03790.03780.00730.10080.02640.01290.1650.09060.01690.3370.07880.09350.18710.09090.123710.6392-8.1409-14.3703
100.00040.0022-0.00150.0074-0.00250.00070.0188-0.00450.01220.0023-0.0012-0.0025-0.017-0.0033-0.01250.3810.07830.10860.040.00290.02059.9589-7.791711.497
110.0708-0.0213-0.03920.0586-0.01840.09120.0257-0.00550.039-0.03430.0483-0.0191-0.12870.0237-0.02370.21240.05190.04050.01920.05350.015411.0189-14.973616.8625
120.0538-0.0203-0.03390.00760.01280.02130.0054-0.0155-0.0037-0.01010.01360.00760.0155-0.0032-0.01560.15270.0409-0.06990.2372-0.04480.105-7.4518-23.949133.8732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:31)
2X-RAY DIFFRACTION2(chain A and resid 32:70)
3X-RAY DIFFRACTION3(chain A and resid 71:101)
4X-RAY DIFFRACTION4(chain A and resid 102:180)
5X-RAY DIFFRACTION5(chain A and resid 181:196)
6X-RAY DIFFRACTION6(chain A and resid 197:226)
7X-RAY DIFFRACTION7(chain A and resid 227:249)
8X-RAY DIFFRACTION8(chain A and resid 250:254)
9X-RAY DIFFRACTION9(chain A and resid 255:266)
10X-RAY DIFFRACTION10(chain A and resid 267:285)
11X-RAY DIFFRACTION11(chain A and resid 286:317)
12X-RAY DIFFRACTION12(chain A and resid 318:322)

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