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- PDB-2g1p: Structure of E. coli DNA adenine methyltransferase (DAM) -

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Basic information

Entry
Database: PDB / ID: 2g1p
TitleStructure of E. coli DNA adenine methyltransferase (DAM)
Components
  • 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
  • DNA adenine methylase
KeywordsTRANSFERASE/DNA / Dam methylation / GATC recognition / Base flipping / Bacterial virulence factor / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type DNA replication initiation / DNA methylation on adenine / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / mismatch repair / response to UV / DNA-dependent DNA replication / sequence-specific DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine modification methylase, M.EcoRV-type / 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 ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine modification methylase, M.EcoRV-type / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (> 10) / DNA / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHorton, J.R. / Liebert, K. / Bekes, M. / Jeltsch, A. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
Authors: Horton, J.R. / Liebert, K. / Bekes, M. / Jeltsch, A. / Cheng, X.
History
DepositionFeb 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Remark 999SEQUENCE AUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA FOR BOTH MOLECULES ...SEQUENCE AUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA FOR BOTH MOLECULES (CHAINS A AND B) BECAUSE OF EXTRA DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
G: 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'
A: DNA adenine methylase
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5037
Polymers71,6424
Non-polymers8613
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)46.2, 71.3, 97.8
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3'


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA adenine methylase / / Deoxyadenosyl-methyltransferase / DNA adenine methyltransferase / M.EcoDam


Mass: 32159.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dam / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P0AEE8, site-specific DNA-methyltransferase (adenine-specific)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM KCl, 10 mM MgSO4, 5-15% PEG400, 100 mM MES or HEPES (pH 6.6-7.4), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgSO411
3PEG40011
4MES11
5HEPES11
6H2O11
7KCl12
8MgSO412
9PEG40012
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 1.89→33.6 Å / Num. all: 51126 / Num. obs: 51126 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.1
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.575 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
GLRFphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modified PDB entry 2DPM
Resolution: 1.89→33.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 303712.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2437 5 %RANDOM
Rwork0.188 ---
all0.188 51126 --
obs0.188 51126 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2817 Å2 / ksol: 0.391587 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.07 Å20 Å20 Å2
2---9 Å20 Å2
3----3.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-35 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.89→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 486 58 314 4859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 1.89→1.92 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 116 5.2 %
Rwork0.278 2123 -
obs-2123 85.5 %

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