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- PDB-5hfj: crystal structure of M1.HpyAVI-SAM complex -

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Basic information

Entry
Database: PDB / ID: 5hfj
Titlecrystal structure of M1.HpyAVI-SAM complex
ComponentsAdenine specific DNA methyltransferase (DpnA)
KeywordsDNA BINDING PROTEIN / M1.HpyAVI / SAM
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / Transferases; Transferring one-carbon groups; Methyltransferases / DNA binding / cytoplasm
Similarity search - Function
Restriction/modification DNA-methyltransferase / DNA methylase N-4/N-6 / DNA methylase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMa, B. / Liu, W. / Zhang, H.
CitationJournal: Oncotarget / Year: 2016
Title: Biochemical and structural characterization of a DNA N6-adenine methyltransferase from Helicobacter pylori
Authors: Ma, B. / Ma, J. / Liu, D. / Guo, L. / Chen, H. / Ding, J. / Liu, W. / Zhang, H.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine specific DNA methyltransferase (DpnA)
B: Adenine specific DNA methyltransferase (DpnA)
C: Adenine specific DNA methyltransferase (DpnA)
D: Adenine specific DNA methyltransferase (DpnA)
E: Adenine specific DNA methyltransferase (DpnA)
F: Adenine specific DNA methyltransferase (DpnA)
G: Adenine specific DNA methyltransferase (DpnA)
H: Adenine specific DNA methyltransferase (DpnA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,31216
Polymers217,1248
Non-polymers3,1878
Water0
1
A: Adenine specific DNA methyltransferase (DpnA)
B: Adenine specific DNA methyltransferase (DpnA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0784
Polymers54,2812
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-11 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: Adenine specific DNA methyltransferase (DpnA)
E: Adenine specific DNA methyltransferase (DpnA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0784
Polymers54,2812
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-8 kcal/mol
Surface area18940 Å2
MethodPISA
3
D: Adenine specific DNA methyltransferase (DpnA)
H: Adenine specific DNA methyltransferase (DpnA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0784
Polymers54,2812
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-12 kcal/mol
Surface area18720 Å2
MethodPISA
4
F: Adenine specific DNA methyltransferase (DpnA)
G: Adenine specific DNA methyltransferase (DpnA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0784
Polymers54,2812
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-9 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.603, 135.603, 265.146
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
Adenine specific DNA methyltransferase (DpnA)


Mass: 27140.543 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0050 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: O24891
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C15H22N6O5S

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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: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 14% PEG2000, 0.2 M lithium sulfate / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97772 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97772 Å / Relative weight: 1
ReflectionResolution: 3.1→48.908 Å / Num. obs: 49903 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/av σ(I): 14 / Net I/σ(I): 14
Reflection shellResolution: 3.1→3.1776 Å / Redundancy: 4 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 1.9 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSmodel building
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HEK
Resolution: 3.1→48.908 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 1996 4.01 %
Rwork0.2212 --
obs0.2234 49833 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 216 0 13194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713540
X-RAY DIFFRACTIONf_angle_d1.65118302
X-RAY DIFFRACTIONf_dihedral_angle_d15.6035130
X-RAY DIFFRACTIONf_chiral_restr0.0671975
X-RAY DIFFRACTIONf_plane_restr0.0072279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17760.3221380.28863374X-RAY DIFFRACTION99
3.1776-3.26340.35371440.27963400X-RAY DIFFRACTION100
3.2634-3.35950.33411410.26373405X-RAY DIFFRACTION100
3.3595-3.46790.31221450.26153427X-RAY DIFFRACTION100
3.4679-3.59180.30451440.26123417X-RAY DIFFRACTION100
3.5918-3.73550.28391410.23963399X-RAY DIFFRACTION100
3.7355-3.90550.29651450.243419X-RAY DIFFRACTION100
3.9055-4.11130.29241420.22713426X-RAY DIFFRACTION100
4.1113-4.36870.28821430.20043434X-RAY DIFFRACTION100
4.3687-4.70580.20161400.17713394X-RAY DIFFRACTION100
4.7058-5.17890.26481380.18883414X-RAY DIFFRACTION100
5.1789-5.92710.26371430.2063451X-RAY DIFFRACTION100
5.9271-7.46330.26021490.22443415X-RAY DIFFRACTION100
7.4633-48.91420.25321430.20523462X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.7762-0.31481.52932.04460.79432.12250.05220.37140.2312-0.6899-0.3609-1.21990.13350.60540.11620.76750.20870.21690.52370.15740.8152-23.1722.8963-26.9158
23.0821-1.25120.16032.0869-1.13931.6573-0.12250.1430.1239-0.1991-0.1970.09370.14240.26410.37610.61750.15920.03910.37620.06320.5007-38.14717.984-19.6938
35.0556-1.41430.59091.7209-0.58272.54070.2746-0.00970.13220.3643-0.0451-0.02750.15930.1483-0.16960.69010.1520.01450.3440.04720.6002-27.63150.8692-11.8736
44.41362.2828-3.21533.5011-0.47773.53140.25990.37550.58980.1083-0.13650.5275-0.3879-0.2217-0.40680.67140.297-0.20080.63750.02570.7752-64.022335.5304-26.0673
53.71830.40331.38374.4005-1.5454.2370.05370.05560.1572-0.61960.15390.295-0.4286-0.1527-0.12550.54190.13640.06860.4420.05730.4443-55.45929.8284-23.864
64.1527-0.6310.68653.239-0.79021.303-0.07770.2970.20210.02790.01970.2023-0.2722-0.00590.10660.58040.1628-0.04210.39030.02510.5064-48.568227.1414-23.1332
73.0296-0.25250.58272.1777-0.62992.7288-0.02240.0802-0.675-0.1706-0.08440.02940.2016-0.27610.20190.58050.2040.00550.40350.00160.6074-49.77612.7748-15.1347
82.46290.4599-0.26442.8786-3.09977.9502-0.3951-0.2891-1.3033-0.12750.21860.3090.63720.5360.24240.82830.33420.10130.34260.21010.9701-44.818833.4299-7.5718
99.4309-1.3372-1.14450.6257-1.03153.1436-0.1594-0.332-1.4065-0.3197-0.22081.14150.1038-0.2830.16970.84210.2652-0.04630.541-0.02270.8918-47.393619.4462-1.1416
101.6581-1.5242.09463.2384-3.56595.6281-1.3172-0.4479-0.67211.30430.85841.0332-0.9642-1.09340.46870.77260.22180.09620.66040.00531.1844-64.783814.4473-14.3239
115.69320.73572.30047.16721.69993.3898-0.331-0.70220.61791.27460.32750.5443-1.1085-0.1544-0.13031.00950.30690.18530.46970.00210.5775-57.164928.643-8.7017
123.80870.1926-1.2973.9161-1.81455.4570.0970.01960.36220.3770.35461.00720.3344-0.2317-0.5420.80680.28420.03860.54060.05150.5536-64.56728.1841-14.846
135.42081.46665.8572.0107-3.51228.705-0.0248-1.1457-0.331-1.4093-0.61940.65250.9865-2.03290.79380.44520.0832-0.0960.8163-0.19231.0381-73.355623.937-19.085
145.17750.1876-0.75492.83440.04034.08330.2968-0.5032-0.43980.8602-0.1567-0.7949-0.09510.1073-0.09470.8816-0.3054-0.10740.49670.09190.5385-24.49-1.048629.6809
152.11531.54341.40463.9735-0.09962.64870.18-0.1732-0.18960.5669-0.141-0.2299-0.15520.2014-0.11090.6436-0.2317-0.00660.40830.0090.5569-38.9374-7.756119.801
165.50950.736-0.70361.4912-0.53582.88420.33450.1541-0.08230.2161-0.089-0.07690.12250.0681-0.22560.7266-0.118-0.00680.31040.00260.4691-26.9621.135713.8843
174.27021.4764-0.38021.37780.24.31350.43450.4888-0.0001-0.799-0.1567-0.3914-0.2456-0.0954-0.31340.93180.29760.02730.5311-0.11210.5737-73.8984-25.1587-15.7047
182.179-1.9939-0.20857.31471.60831.84920.18270.0547-0.0504-0.4920.0896-0.1855-0.12420.1975-0.20520.79270.1738-0.01080.4433-0.0220.5492-86.3395-10.9323-11.8669
193.52051.80220.05694.3056-0.54381.2057-0.0274-0.5925-0.10610.8560.23070.4085-0.7019-0.2106-0.43810.97440.22710.12070.6407-0.06770.9208-88.6683-16.3482.4318
205.43370.2192-0.73670.12011.08284.42380.43480.0323-0.054-0.4241-0.3597-0.4195-0.43210.25440.02870.73740.12720.08310.33890.05670.5512-71.7962-19.2428-4.5238
214.5901-4.08952.7064.5422-3.25613.13430.4031-0.6078-0.58331.4254-0.830.97690.0397-0.04280.19561.0564-0.32560.01880.70930.00090.557-62.6295-33.851328.707
223.08052.0286-0.04294.78030.23512.03290.434-0.49640.12940.7914-0.46720.2508-0.0737-0.1640.01990.7006-0.1844-0.02640.42390.00930.5942-48.8134-20.872721.0682
232.2658-3.929-5.16153.18892.74953.86560.46661.00550.0129-0.0532-0.5383-0.2051-0.3942-0.8536-0.30170.8881-0.0604-0.19520.7479-0.17480.9237-54.252-14.42919.5696
246.84390.67951.37244.5752-1.88663.5440.5636-0.3054-0.00220.5564-0.47060.7308-0.3618-0.3848-0.27370.6712-0.07460.09630.3001-0.02980.5644-63.2652-25.33116.4588
255.1088-0.54882.23716.79232.25754.8578-0.24740.08250.32440.10690.44521.96070.2408-0.6082-0.07680.7468-0.225-0.0170.50860.08390.8892-106.42625.840635.552
263.44561.9905-0.35215.11381.51154.2381-0.00160.08910.4712-0.26160.12520.279-0.2441-0.282-0.12460.501-0.1002-0.13460.33330.0340.5575-89.951112.92627.3401
278.51430.8309-4.12686.15422.45538.84-0.478-0.5459-1.39490.3174-0.2612-0.31561.64380.3360.76240.9282-0.2693-0.27170.57350.11840.9815-86.6774-4.329633.9674
284.81170.9607-0.22945.21250.8952.82540.11510.11610.2543-0.58380.14650.00090.171-0.2234-0.26830.7041-0.1872-0.14740.44810.03580.5334-99.37831.788121.3184
295.7368-3.3091-1.17866.40293.33033.54090.33730.44950.13470.66520.2572-1.535-0.4621-0.0357-0.23280.5261-0.2519-0.24040.6372-0.10630.9384-65.994638.313737.6742
303.38640.1287-0.14361.02351.49623.47410.0024-0.5234-0.06340.38120.0849-0.25450.26410.18270.01360.4633-0.0459-0.10990.47060.03390.5689-74.898130.364937.2548
314.87512.3582-0.76495.37370.12071.86020.1041-0.1240.2660.7937-0.0808-0.36540.038-0.18570.06270.5733-0.0907-0.10950.37250.04250.5909-80.98429.704332.9611
321.58821.2503-1.09769.44250.77821.4136-0.50860.0445-0.5421-0.12970.9017-1.6230.58010.3555-0.25410.6658-0.0539-0.17220.6696-0.20080.9695-77.653714.14726.219
332.15950.9957-0.07564.48310.1480.629-0.46240.3792-0.4787-0.38050.63860.263-0.1282-0.0092-0.02470.807-0.2367-0.10160.4767-0.11290.6314-80.632222.573623.1665
343.4602-1.49680.52921.28970.57293.29780.08740.4086-0.2801-0.70050.0373-1.15621.45090.18370.03380.9571-0.15130.22390.63250.04411.2346-69.830217.153720.8919
355.59012.0506-0.14794.21012.5911.9286-0.16910.3536-0.0486-0.19430.497-0.9325-0.18840.5152-0.35720.5399-0.1748-0.01040.446-0.04550.7239-66.514829.68824.3363
365.00641.6472-1.48319.9722-1.64686.2162-0.3254-1.4575-0.0429-0.0387-0.647-0.7854-0.18281.41790.9040.4555-0.1713-0.18640.9653-0.06781.3809-55.938625.630134.1382
373.5491-1.1254-0.7153.13780.10192.91810.22240.5228-0.4489-0.8343-0.20850.5435-0.1609-0.50820.03190.86290.2699-0.14860.5348-0.11170.6323-104.51034.1434-19.441
385.6374-5.203-5.637.15868.84712.0602-0.0246-0.2827-0.91970.3017-1.37911.4185-0.6557-1.15321.3190.97850.33590.04590.90160.19371.1372-98.8943-14.53113.2292
393.7126-0.3374-0.25292.9963-0.76831.71580.1598-0.16760.0398-0.3409-0.1125-0.17680.04970.0995-0.12290.79380.2074-0.04290.4547-0.12440.4869-97.51817.6246-6.0407
403.8578-1.2142-0.64190.42320.51071.34320.24740.188-0.76520.1943-0.11630.4210.0999-0.2933-0.0460.6940.158-0.09480.46880.03130.6099-113.84379.0854-9.2906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 231 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 18 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 63 )
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 97 )
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 134 )
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 144 )
9X-RAY DIFFRACTION9chain 'B' and (resid 145 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 173 )
11X-RAY DIFFRACTION11chain 'B' and (resid 174 through 193 )
12X-RAY DIFFRACTION12chain 'B' and (resid 194 through 218 )
13X-RAY DIFFRACTION13chain 'B' and (resid 219 through 229 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 82 )
15X-RAY DIFFRACTION15chain 'C' and (resid 83 through 144 )
16X-RAY DIFFRACTION16chain 'C' and (resid 145 through 231 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 60 )
18X-RAY DIFFRACTION18chain 'D' and (resid 61 through 134 )
19X-RAY DIFFRACTION19chain 'D' and (resid 135 through 173 )
20X-RAY DIFFRACTION20chain 'D' and (resid 174 through 231 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 18 )
22X-RAY DIFFRACTION22chain 'E' and (resid 19 through 144 )
23X-RAY DIFFRACTION23chain 'E' and (resid 145 through 173 )
24X-RAY DIFFRACTION24chain 'E' and (resid 174 through 230 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 72 )
26X-RAY DIFFRACTION26chain 'F' and (resid 73 through 134 )
27X-RAY DIFFRACTION27chain 'F' and (resid 135 through 144 )
28X-RAY DIFFRACTION28chain 'F' and (resid 145 through 231 )
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 18 )
30X-RAY DIFFRACTION30chain 'G' and (resid 19 through 63 )
31X-RAY DIFFRACTION31chain 'G' and (resid 64 through 97 )
32X-RAY DIFFRACTION32chain 'G' and (resid 98 through 119 )
33X-RAY DIFFRACTION33chain 'G' and (resid 120 through 144 )
34X-RAY DIFFRACTION34chain 'G' and (resid 145 through 173 )
35X-RAY DIFFRACTION35chain 'G' and (resid 174 through 218 )
36X-RAY DIFFRACTION36chain 'G' and (resid 219 through 229 )
37X-RAY DIFFRACTION37chain 'H' and (resid 1 through 110 )
38X-RAY DIFFRACTION38chain 'H' and (resid 111 through 125 )
39X-RAY DIFFRACTION39chain 'H' and (resid 126 through 184 )
40X-RAY DIFFRACTION40chain 'H' and (resid 185 through 230 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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