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

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Basic information

Entry
Database: PDB / ID: 4gon
TitleCrystal Structure of E. coli DNA Adenine Methyltransferase in Complex with Indole Aza-SAM
ComponentsDNA adenine methylase
KeywordsTRANSFERASE / methylation
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-templated 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
Chem-0Y1 / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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

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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)97,9626
Polymers96,4313
Non-polymers1,5323
Water54030
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)32,6542
Polymers32,1441
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6542
Polymers32,1441
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6542
Polymers32,1441
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)161.315, 161.315, 95.134
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-0Y1 / 5'-{[(3S)-3-amino-3-carboxypropyl][2-(1H-indol-3-yl)ethyl]amino}-5'-deoxyadenosine


Mass: 510.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H30N8O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.71 Å3/Da / Density % sol: 66.81 %
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: 2.712→35.897 Å / Num. all: 38865 / Num. obs: 38865 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rsym value: 0.066 / Net I/σ(I): 21
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.71-2.786.30.73310.733199.9
2.78-2.866.30.5591.40.559199.6
2.86-2.946.30.461.60.46199.9
2.94-3.036.30.3662.10.366199.3
3.03-3.136.30.2862.60.2861100
3.13-3.246.30.1953.90.195199.9
3.24-3.366.20.1395.40.139199.7
3.36-3.56.10.1096.90.109199.8
3.5-3.666.20.0819.30.081199.8
3.66-3.846.20.06210.20.062199.8
3.84-4.046.20.051140.051199.6
4.04-4.296.20.04416.40.044199.9
4.29-4.586.10.03420.90.034199.6
4.58-4.955.90.03122.50.031199.5
4.95-5.4260.0323.50.03199.9
5.42-6.066.20.03321.30.0331100
6.06-76.20.03122.80.0311100
7-8.586.10.022300.022199.8
8.58-12.135.90.01834.80.018199.9
12.13-35.89750.01930.60.019194.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→30.04 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.61 / SU ML: 0.203 / SU R Cruickshank DPI: 0.4239 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25777 1934 5 %RANDOM
Rwork0.21011 ---
obs0.21249 36479 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.72→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 111 30 6180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9818600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4155722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21423.223332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1721548
X-RAY DIFFRACTIONr_chiral_restr0.1330.2886
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1831.53670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24325895
X-RAY DIFFRACTIONr_scbond_it2.83532670
X-RAY DIFFRACTIONr_scangle_it4.7154.52705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.721→2.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 159 -
Rwork0.268 2580 -
obs--96.72 %

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