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- PDB-4gol: Crystal Structure of E. coli DNA Adenine Methyltransferase in Com... -

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Basic information

Entry
Database: PDB / ID: 4gol
TitleCrystal Structure of E. coli DNA Adenine Methyltransferase in Complex with Methylated Aza-SAM
ComponentsDNA adenine methylase
KeywordsTRANSFERASE / Methylation
Function / homology
Function and homology information


bacterial-type DNA replication initiation / macromolecule modification / 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 / methylation / 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-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsHarmer, J.E. / Roach, P.L.
CitationJournal: To be Published
Title: Structural Basis of Selective N-6 adenine methyltransferase Inhibition by Transition State Mimic
Authors: Harmer, J.E. / McKelvie, J.C. / Hobley, G. / Roach, P.L.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)97,5756
Polymers96,4313
Non-polymers1,1443
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5252
Polymers32,1441
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5252
Polymers32,1441
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5252
Polymers32,1441
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.970, 160.970, 96.029
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 / DNA adenine methyltransferase / Deoxyadenosyl-methyltransferase / M.EcoDam


Mass: 32143.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b3387, dam, JW3350 / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEE8, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MES, 1600 mM ammonium Sulfate, 14-18% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92453 Å / Relative weight: 1
ReflectionResolution: 2.539→35.873 Å / Num. all: 47602 / Num. obs: 47602 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rsym value: 0.077 / Net I/σ(I): 18.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.54-2.66.20.78112173434890.781100
2.6-2.686.30.5991.32124033890.599100
2.68-2.756.20.5191.52072933260.519100
2.75-2.846.30.4021.91991331830.402100
2.84-2.936.30.3262.31968331330.326100
2.93-3.036.30.2612.91887830140.261100
3.03-3.156.30.2023.81823929080.202100
3.15-3.286.30.15351769028150.153100
3.28-3.426.30.10971698827050.109100
3.42-3.596.30.0829.21620225820.082100
3.59-3.786.30.06112.31532024500.061100
3.78-4.016.20.05114.61446923310.051100
4.01-4.2960.04217.21320021930.042100
4.29-4.6360.03321.21245020600.033100
4.63-5.086.20.03321.11180919070.033100
5.08-5.686.20.03420.51063217130.034100
5.68-6.556.20.03321.1929315040.033100
6.55-8.036.10.02723.9810813220.027100
8.03-11.3560.0226.8604910160.02100
11.35-35.8735.10.0228.728865620.0295.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→29.09 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2213 / WRfactor Rwork: 0.1867 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8461 / SU B: 6.65 / SU ML: 0.151 / SU R Cruickshank DPI: 0.3108 / SU Rfree: 0.2436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 2263 4.9 %RANDOM
Rwork0.2088 ---
obs0.2107 45751 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.53 Å2 / Biso mean: 44.5173 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.57→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 81 18 6138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226288
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9728525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3723.223332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.204151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9361548
X-RAY DIFFRACTIONr_chiral_restr0.1290.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214909
X-RAY DIFFRACTIONr_mcbond_it1.2331.53670
X-RAY DIFFRACTIONr_mcangle_it2.33625895
X-RAY DIFFRACTIONr_scbond_it3.30232618
X-RAY DIFFRACTIONr_scangle_it5.2874.52630
LS refinement shellResolution: 2.572→2.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 150 -
Rwork0.258 3191 -
all-3341 -
obs--99.35 %

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