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- PDB-4rto: Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) w... -

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Basic information

Entry
Database: PDB / ID: 4rto
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with Sinefungin and with DNA Containing Proximal Pap Regulon Sequence
Components
  • DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-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: 2.69 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*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')
G: DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4174
Polymers41,0353
Non-polymers3811
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.936, 63.254, 143.211
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*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')


Mass: 3372.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')


Mass: 3332.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 16% PEG200, 100mM KCl, 10mM MgSO4, 100mM HEPES buffer, pH 6.8, 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 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→34.9 Å / Num. all: 9617 / Num. obs: 9617 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.4
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / Num. unique all: 952 / % possible all: 99.6

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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: 2.69→34.855 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 506 5.29 %RANDOM
Rwork0.2177 ---
obs0.2195 9564 99.12 %-
all-9564 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→34.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 445 27 19 2448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022539
X-RAY DIFFRACTIONf_angle_d0.4833551
X-RAY DIFFRACTIONf_dihedral_angle_d18.101912
X-RAY DIFFRACTIONf_chiral_restr0.019387
X-RAY DIFFRACTIONf_plane_restr0.002384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.95910.31651390.3072157X-RAY DIFFRACTION98
2.9591-3.3870.3051070.24862249X-RAY DIFFRACTION100
3.387-4.2660.24641300.20052260X-RAY DIFFRACTION100
4.266-34.85830.21621300.19862392X-RAY DIFFRACTION99
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)
15.06023.75793.88483.55331.82914.88280.0568-0.77260.093-0.7408-0.39250.74150.9062-0.47880.45020.56120.1089-0.09140.52610.01620.5751-12.85873.248391.7545
22.9542-1.334-1.15082.966-0.50914.51530.40760.5301-0.461-0.46880.10890.82420.3799-0.7272-0.47720.4273-0.0273-0.1790.39770.0470.6289-9.4358-7.440893.474
34.37211.38340.1866.5188-2.21616.5443-0.1999-0.42010.37580.47220.2513-0.017-0.177-0.2124-0.0490.21610.060.00940.2638-0.02710.3735-3.458911.1987105.7334
43.1740.5882-0.30327.5863-0.80133.64350.10510.0627-0.21410.03560.08040.60040.1176-0.2554-0.19390.20620.0361-0.06370.43420.06390.302-7.67514.31100.5969
55.606-1.60540.47175.3739-1.2743.94760.5020.6555-0.5864-1.0433-0.2904-0.05721.08750.6362-0.19090.71090.1753-0.11310.6413-0.07420.4783-0.7092-9.898982.7296
62.6421-3.1075-0.05269.6369-1.76140.49920.81520.572-0.0252-1.583-0.75330.21821.03090.4764-0.24150.97210.1693-0.15680.9128-0.18780.6652-7.3558-4.766972.6383
76.8487-1.1394-2.66592.96310.17814.7232-0.98091.4481.2143-0.26490.5994-0.32090.0673-0.09720.48030.4089-0.1229-0.01530.75630.05930.69120.026218.619385.4771
82.2584-3.1871-1.83814.91931.84094.0714-0.68261.17710.6882-0.32930.3062-0.70560.19720.46730.31310.4139-0.04290.11560.79370.08980.64917.328318.509485.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:17 )A3 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:68 )A18 - 68
3X-RAY DIFFRACTION3( CHAIN A AND RESID 69:126 )A69 - 126
4X-RAY DIFFRACTION4( CHAIN A AND RESID 127:162 )A127 - 162
5X-RAY DIFFRACTION5( CHAIN A AND RESID 163:228 )A163 - 228
6X-RAY DIFFRACTION6( CHAIN A AND RESID 229:270 )A229 - 270
7X-RAY DIFFRACTION7( CHAIN F AND RESID 1:11 )F1 - 11
8X-RAY DIFFRACTION8( CHAIN G AND RESID 1:11 )G1 - 11

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