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- PDB-5hek: crystal structure of M1.HpyAVI -

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Basic information

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


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / 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
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMa, B. / Zhang, H. / Liu, W.
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 6, 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

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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)


Theoretical massNumber of molelcules
Total (without water)112,8474
Polymers112,8474
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-26 kcal/mol
Surface area35040 Å2
2
A: Adenine specific DNA methyltransferase (DpnA)
C: Adenine specific DNA methyltransferase (DpnA)


Theoretical massNumber of molelcules
Total (without water)56,4232
Polymers56,4232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-13 kcal/mol
Surface area18480 Å2
MethodPISA
3
B: Adenine specific DNA methyltransferase (DpnA)
D: Adenine specific DNA methyltransferase (DpnA)


Theoretical massNumber of molelcules
Total (without water)56,4232
Polymers56,4232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-8 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.725, 69.725, 532.752
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
Adenine specific DNA methyltransferase (DpnA)


Mass: 28211.697 Da / Num. of mol.: 4
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 / Production host: Escherichia coli (E. coli) / References: UniProt: O24891

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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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 1.4 M ammonium tartrate / PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.093 Å / Num. obs: 27750 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.065 / Net I/σ(I): 12.1
Reflection shellResolution: 3.01→3.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G60

1g60


Resolution: 3→49.093 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3083 1257 4.61 %
Rwork0.2508 --
obs0.2534 27243 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 0 0 6166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076314
X-RAY DIFFRACTIONf_angle_d1.4088515
X-RAY DIFFRACTIONf_dihedral_angle_d14.9852361
X-RAY DIFFRACTIONf_chiral_restr0.061924
X-RAY DIFFRACTIONf_plane_restr0.0091065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.12010.34011390.27652865X-RAY DIFFRACTION100
3.1201-3.26210.36511380.27842850X-RAY DIFFRACTION100
3.2621-3.4340.33371390.29092862X-RAY DIFFRACTION100
3.434-3.64910.41121400.32642908X-RAY DIFFRACTION99
3.6491-3.93070.42771150.33342368X-RAY DIFFRACTION82
3.9307-4.32610.27751410.23412931X-RAY DIFFRACTION100
4.3261-4.95160.25211430.18392956X-RAY DIFFRACTION100
4.9516-6.23650.28161460.21673026X-RAY DIFFRACTION100
6.2365-49.09980.25151560.23293220X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -18.0304 Å / Origin y: 17.0395 Å / Origin z: -33.3439 Å
111213212223313233
T0.359 Å20.1603 Å20.0138 Å2-0.1959 Å20.0004 Å2--0.263 Å2
L0.1747 °20.1108 °2-0.0151 °2-0.2256 °20.0108 °2--0.5207 °2
S-0.0733 Å °-0.103 Å °-0.0095 Å °-0.0014 Å °0.0843 Å °-0.0144 Å °0.0038 Å °0.0261 Å °-0.0149 Å °
Refinement TLS groupSelection details: all

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