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- PDB-4h0n: Crystal structure of Spodoptera frugiperda DNMT2 E260A/E261A/K263... -

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Basic information

Entry
Database: PDB / ID: 4h0n
TitleCrystal structure of Spodoptera frugiperda DNMT2 E260A/E261A/K263A mutant
ComponentsDNMT2TRNA (cytosine38-C5)-methyltransferase
KeywordsTRANSFERASE / SAH binding
Function / homology
Function and homology information


methyltransferase activity / methylation
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
S-ADENOSYL-L-HOMOCYSTEINE / SFRICE_001256
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.712 Å
AuthorsLi, S. / Du, J. / Yang, H. / Yin, J. / Zhong, J. / Ding, J.
CitationJournal: J Mol Cell Biol / Year: 2013
Title: Functional and structural characterization of DNMT2 from Spodoptera frugiperda.
Authors: Li, S. / Du, J. / Yang, H. / Yin, J. / Ding, J. / Zhong, J.
History
DepositionSep 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: DNMT2
B: DNMT2
C: DNMT2
D: DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,51212
Polymers153,8144
Non-polymers1,6988
Water3,495194
1
A: DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8783
Polymers38,4531
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8783
Polymers38,4531
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8783
Polymers38,4531
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8783
Polymers38,4531
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.394, 106.154, 151.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DNMT2 / TRNA (cytosine38-C5)-methyltransferase / DNA methyltransferase


Mass: 38453.441 Da / Num. of mol.: 4 / Mutation: E260A/E261A/K263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Strain: SF9 / Gene: DNMT2 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: A0A2H1VE33*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M calcium chloride, 0.1 M HEPES, pH 6.8, 16% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 42837 / Num. obs: 42751 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.69 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G55

1g55


Resolution: 2.712→48.697 Å / SU ML: 0.32 / σ(F): 1.36 / σ(I): 0 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 2144 5.04 %RANDOM
Rwork0.2018 ---
obs0.2045 42563 98.75 %-
all-44707 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.476 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6433 Å2-0 Å2-0 Å2
2---6.4992 Å2-0 Å2
3----6.144 Å2
Refinement stepCycle: LAST / Resolution: 2.712→48.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10736 0 108 194 11038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511084
X-RAY DIFFRACTIONf_angle_d0.91914996
X-RAY DIFFRACTIONf_dihedral_angle_d16.924212
X-RAY DIFFRACTIONf_chiral_restr0.0651668
X-RAY DIFFRACTIONf_plane_restr0.0041904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.712-2.7750.29461010.24992357X-RAY DIFFRACTION88
2.775-2.84440.31811580.27092648X-RAY DIFFRACTION100
2.8444-2.92130.351340.27322691X-RAY DIFFRACTION100
2.9213-3.00730.36581460.25692685X-RAY DIFFRACTION100
3.0073-3.10430.32321360.24872693X-RAY DIFFRACTION100
3.1043-3.21520.30121330.23962722X-RAY DIFFRACTION100
3.2152-3.34390.29571530.22232675X-RAY DIFFRACTION100
3.3439-3.49610.29291360.20362709X-RAY DIFFRACTION100
3.4961-3.68040.27111550.18592703X-RAY DIFFRACTION100
3.6804-3.91080.20711650.17122709X-RAY DIFFRACTION100
3.9108-4.21270.18961420.16152736X-RAY DIFFRACTION100
4.2127-4.63630.18931450.14622751X-RAY DIFFRACTION100
4.6363-5.30650.21761380.15562748X-RAY DIFFRACTION100
5.3065-6.68280.27811450.22992787X-RAY DIFFRACTION100
6.6828-48.70480.21491570.20142805X-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)
11.13421.6852-0.11983.5824-0.91390.96440.1384-0.07190.1309-0.2503-0.06580.42580.0481-0.3154-0.06570.21620.0049-0.07960.23570.02420.307594.5961115.7637159.3462
24.2662-2.1672-1.79046.22091.252.9312-0.07070.2144-0.42210.03670.0620.42480.3345-0.22740.13140.3785-0.1034-0.00660.2622-0.01990.1689105.4428112.2806154.1205
33.5543-0.8631-1.31286.13673.08853.86-0.1520.0061-0.21650.73430.17470.0560.2797-0.05890.13750.2778-0.01980.0290.28280.00620.2543108.023110.2371146.4416
43.1915-1.0121-0.39853.1734-0.75693.78660.18630.1282-0.11890.0983-0.1229-0.081-0.32470.3714-0.1160.2079-0.0253-0.03670.1798-0.03440.1944113.2353119.1657157.0638
50.4010.7636-0.54114.0547-1.77552.87530.1086-0.02910.0328-0.0132-0.1033-0.1465-0.380.17840.04910.2844-0.02090.01960.1921-0.04170.2427112.3594118.6006171.8303
65.95921.68932.18235.01470.51233.29130.0748-0.9345-0.481-0.133-0.19740.43160.1564-0.22830.14830.3644-0.0579-0.07290.33790.07910.301103.17890.2779180.561
75.5740.16252.29784.0249-2.82593.7924-0.30620.2173-0.16-0.8099-0.00290.05510.9180.64210.3730.5723-0.01840.00080.21230.03260.2478105.900893.6407175.193
85.4992-2.237-1.59522.31832.15856.68-0.2193-0.6064-1.20890.37450.21760.38080.57790.9522-0.02520.3541-0.049-0.06380.42360.12890.4051110.765579.5205184.9754
91.5229-0.3183-0.0484.3045-1.82111.53430.1624-0.1629-0.0556-0.0457-0.13550.48430.2322-0.2468-0.00860.2727-0.02340.02560.2082-0.02370.247198.5891105.6599172.4372
102.0534-0.9237-0.01672.50880.11361.4216-0.14070.09040.04070.1730.26730.36690.3227-0.445-0.10640.2273-0.08330.05670.42190.11830.2434107.477599.0233211.3435
111.9296-0.0560.6592.27840.05782.5045-0.2435-0.25480.14040.16410.138-0.06-0.0863-0.15780.03370.27590.0576-0.0030.26740.01350.2182122.49499.2534217.8123
120.6984-1.15420.69383.9518-0.50341.43970.06690.1443-0.0157-0.1275-0.0946-0.16660.1542-0.08720.0140.24670.0120.05910.2562-0.00520.1929125.1746101.669198.8566
130.40920.82570.06484.7457-0.46210.4519-0.0306-0.01850.17930.42170.1550.2169-0.0879-0.1644-0.12070.29360.05170.02990.3070.04640.2574114.442125.6319201.7647
141.62750.7256-0.03763.2034-0.22972.3946-0.03750.13860.017-0.46490.11720.46270.2388-0.3363-0.1650.3644-0.0923-0.10190.33510.10870.3283142.9308115.819161.2924
153.3838-1.6851-2.00322.39022.35454.8912-0.09410.3968-0.5199-0.36820.02290.3340.2871-0.1580.06220.5186-0.1579-0.04290.33810.02520.3334154.4713108.3517151.6631
162.68120.1196-0.08983.47260.26092.7112-0.01850.1951-0.1225-0.12230.21390.21590.25840.0755-0.20030.3747-0.07470.02240.2385-0.0230.1722160.1068118.5761156.4631
170.66690.8079-0.82833.7713-1.76592.91680.0376-0.0837-0.0142-0.183-0.1527-0.16060.05470.34840.09990.37430.0041-0.02890.235-0.03640.2002161.1765118.2834172.8507
186.841.8162.02945.52720.51834.9492-0.0721-0.5123-0.49610.08230.23830.14520.1779-0.2129-0.03540.260.02550.03460.25250.09140.2471151.995989.8987181.6927
193.84090.87341.8136.2118-4.66438.70940.15550.193-0.2261-0.58630.50490.34780.86270.3203-0.23760.4385-0.0384-0.01530.21690.04740.2715154.654293.4087176.5478
206.7839-1.8687-0.27246.1320.25836.6482-0.2241-0.0322-0.9114-0.26070.0423-0.12670.54370.26790.10410.45960.00960.02880.3250.13440.4295159.546379.0729185.9359
211.23070.53090.17814.8698-2.05970.8112-0.0664-0.0174-0.0792-0.42380.22720.73640.0096-0.0305-0.17070.2593-0.0110.00850.25930.02510.2979147.3498105.4026174.0598
222.2237-0.83380.85041.2720.171.7191-0.0718-0.09360.08270.3860.08630.0901-0.0131-0.07310.00610.38890.01760.050.22710.02480.2206165.05899.6779216.1557
230.511-0.66510.08574.164-0.84521.089-0.03390.01830.07990.29990.0003-0.0025-0.1295-0.11880.00440.26730.02930.03130.27370.00520.219166.7708118.5955201.9678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:66)
2X-RAY DIFFRACTION2chain 'A' and (resseq 67:84)
3X-RAY DIFFRACTION3chain 'A' and (resseq 85:107)
4X-RAY DIFFRACTION4chain 'A' and (resseq 108:138)
5X-RAY DIFFRACTION5chain 'A' and (resseq 139:197)
6X-RAY DIFFRACTION6chain 'A' and (resseq 198:228)
7X-RAY DIFFRACTION7chain 'A' and (resseq 229:251)
8X-RAY DIFFRACTION8chain 'A' and (resseq 252:279)
9X-RAY DIFFRACTION9chain 'A' and (resseq 280:332)
10X-RAY DIFFRACTION10chain 'B' and (resseq 2:66)
11X-RAY DIFFRACTION11chain 'B' and (resseq 67:137)
12X-RAY DIFFRACTION12chain 'B' and (resseq 138:197)
13X-RAY DIFFRACTION13chain 'B' and (resseq 198:332)
14X-RAY DIFFRACTION14chain 'C' and (resseq 2:66)
15X-RAY DIFFRACTION15chain 'C' and (resseq 67:97)
16X-RAY DIFFRACTION16chain 'C' and (resseq 98:137)
17X-RAY DIFFRACTION17chain 'C' and (resseq 138:197)
18X-RAY DIFFRACTION18chain 'C' and (resseq 198:228)
19X-RAY DIFFRACTION19chain 'C' and (resseq 229:251)
20X-RAY DIFFRACTION20chain 'C' and (resseq 252:279)
21X-RAY DIFFRACTION21chain 'C' and (resseq 280:332)
22X-RAY DIFFRACTION22chain 'D' and (resseq 2:137)
23X-RAY DIFFRACTION23chain 'D' and (resseq 138:332)

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