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- PDB-4rtj: A non-cognate complex of Escherichia coli DNA Adenine Methyltrans... -

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Basic information

Entry
Database: PDB / ID: 4rtj
TitleA non-cognate complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with DNA and Sinefungin
Components
  • DNA (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 / methylation-independent transcriptional repressor / Transferase-DNA complex
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 / DNA restriction-modification system / 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
SINEFUNGIN / DNA / DNA (> 10) / : / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHorton, J.R. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
Authors: Horton, J.R. / Zhang, X. / Blumenthal, R.M. / Cheng, X.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 20, 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
A: DNA adenine methylase
F: DNA (5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3')
G: DNA (5'-D(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0975
Polymers41,6543
Non-polymers4432
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.367, 63.114, 145.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA adenine methylase


Mass: 34330.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MDS42 / Gene: dam, ECMDS42_2833 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: H0Q7C9, UniProt: P0AEE8*PLUS
#2: DNA chain DNA (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 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA BECAUSE OF EXTRA DENSITY.

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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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 289 K / pH: 7.2
Details: 18% PEG200, 100mM KCl, 10mM MgSO4, 100mM MES buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 5, 2005 / Details: SI(111)
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→32.509 Å / Num. obs: 23469 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.9
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.5 / % possible all: 98

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Processing

Software
NameVersionClassification
SERGUIdata collection
GLRFphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G1P

2g1p


Resolution: 1.99→32.5 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1132 4.84 %
Rwork0.214 --
obs0.215 23412 98.4 %
all-23412 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 486 31 97 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032646
X-RAY DIFFRACTIONf_angle_d0.5853693
X-RAY DIFFRACTIONf_dihedral_angle_d18.216976
X-RAY DIFFRACTIONf_chiral_restr0.023398
X-RAY DIFFRACTIONf_plane_restr0.003394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.07930.28691340.26622697X-RAY DIFFRACTION97
2.0793-2.18890.2521370.24622707X-RAY DIFFRACTION97
2.1889-2.3260.25161660.24672693X-RAY DIFFRACTION98
2.326-2.50550.26151310.24442765X-RAY DIFFRACTION99
2.5055-2.75760.2751320.2442798X-RAY DIFFRACTION99
2.7576-3.15630.25151330.23852834X-RAY DIFFRACTION100
3.1563-3.97550.22511320.19212856X-RAY DIFFRACTION100
3.9755-32.51290.21661670.19352930X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.65820.57280.70431.97870.54023.12350.36420.5074-0.5152-0.6577-0.16050.8810.1692-0.6015-0.13270.46540.0561-0.20550.5699-0.02740.625-12.7497-3.559989.9391
23.1639-0.3350.90264.0762-0.28022.75050.0876-0.1295-0.13770.12240.04240.20940.0557-0.2649-0.110.19340.0352-0.030.25440.02710.2475-5.22013.4341102.1932
34.8726-0.449-0.47414.3584-0.3773.99640.74821.7096-0.7058-0.7761-0.47850.16770.64910.1716-0.20930.68490.2715-0.1570.9136-0.23230.4826-3.2514-5.862678.0537
45.55050.14482.65048.32240.24757.2649-0.51721.32051.0483-0.36720.1923-0.42820.2114-0.07780.15740.3491-0.01960.05030.6470.17710.546219.795417.514786.3693
57.45883.3489-0.75233.4503-2.20125.3088-0.5350.79140.3889-0.16480.1958-0.3287-0.01030.1950.15340.35370.0028-0.06140.47610.14450.587318.537919.074488.0119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:39 )A3 - 39
2X-RAY DIFFRACTION2( CHAIN A AND RESID 40:180 )A40 - 180
3X-RAY DIFFRACTION3( CHAIN A AND RESID 181:270 )A181 - 270
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1:12 )F1 - 12
5X-RAY DIFFRACTION5( CHAIN G AND RESID 1:12 )G1 - 12

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