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- PDB-2ore: Binary Structure of Escherichia coli DNA Adenine Methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 2ore
TitleBinary Structure of Escherichia coli DNA Adenine Methyltransferase and S-adenosylhomocysteine
ComponentsDNA adenine methylase
KeywordsTRANSFERASE / DAM METHYLATION / GATC RECOGNITION / S-ADENOSYLHOMOCYSTEINE CONFORMATION / BACTERIAL VIRULENCE FACTOR
Function / homology
Function and homology information


bacterial-type DNA replication initiation / : / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / mismatch repair / response to UV / DNA-templated DNA replication / sequence-specific DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / 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 ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsHorton, J.R. / Cheng, X.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Two Alternative Conformations of S-Adenosyl-L-homocysteine Bound to Escherichia coli DNA Adenine Methyltransferase and the Implication of Conformational Changes in Regulating the Catalytic Cycle.
Authors: Liebert, K. / Horton, J.R. / Chahar, S. / Orwick, M. / Cheng, X. / Jeltsch, A.
#1: Journal: 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 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / 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
D: DNA adenine methylase
E: DNA adenine methylase
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1947
Polymers102,9453
Non-polymers1,2494
Water41423
1
D: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6992
Polymers34,3151
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6992
Polymers34,3151
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7953
Polymers34,3151
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.135, 160.135, 94.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA adenine methylase / / Deoxyadenosyl-methyltransferase / DNA adenine methyltransferase / M.EcoDam


Mass: 34314.961 Da / Num. of mol.: 3
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)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.5 M lithium sulfate,50mM magnesium sulfate, 100mM HEPES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97923 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.99→34.67 Å / Num. all: 28266 / Num. obs: 28125 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.99→3.1 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
GLRFphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G1P

2g1p


Resolution: 2.99→34.67 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1416 -RANDOM
Rwork0.202 ---
all0.205 28266 --
obs0.202 28125 99.5 %-
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.74 Å20.85 Å20 Å2
2---8.42 Å20 Å2
3---17.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-34.67 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.99→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5868 0 135 23 6026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.9

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