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

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Basic information

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


Theoretical massNumber of molelcules
Total (without water)41,4184
Polymers41,0363
Non-polymers3811
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.333, 66.296, 149.241
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*AP*AP*GP*AP*TP*CP*G)-3')


Mass: 3357.223 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*G)-3')


Mass: 3348.209 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 / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 24% PEG200, 100mM KCl, 10mM MgSO4, 100mM MES 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-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / 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: 2.19→27.606 Å / Num. all: 20122 / Num. obs: 20122 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.4
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1955 / % possible all: 98.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
SOLVEphasing
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: 2.193→27.6 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1003 5 %RANDOM
Rwork0.2038 ---
obs0.2062 20061 98.98 %-
all-20061 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 445 27 88 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112627
X-RAY DIFFRACTIONf_angle_d1.0793665
X-RAY DIFFRACTIONf_dihedral_angle_d18.615966
X-RAY DIFFRACTIONf_chiral_restr0.048394
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.193-2.30870.30911380.24372606X-RAY DIFFRACTION97
2.3087-2.45320.30171390.24112659X-RAY DIFFRACTION98
2.4532-2.64250.32821410.24772671X-RAY DIFFRACTION99
2.6425-2.90820.33941420.25582711X-RAY DIFFRACTION99
2.9082-3.32840.30971450.25542745X-RAY DIFFRACTION100
3.3284-4.1910.22111470.18222777X-RAY DIFFRACTION100
4.191-27.60850.19551510.16192889X-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)
14.26010.2120.94883.39551.33844.13140.09870.1922-0.2201-0.2074-0.03510.56290.3655-0.7719-0.03430.3042-0.0465-0.10170.36070.0580.31736.6399-6.1194168.84
22.23980.88030.65454.0826-0.82122.7163-0.0217-0.24050.03430.26830.1370.3011-0.1399-0.3009-0.11180.21290.0628-0.00430.25940.01770.198814.05527.2745182.8173
34.4925-0.65910.46024.345-0.4394.92130.44320.9002-0.2824-0.7639-0.19980.03550.64210.3492-0.17170.5160.1363-0.04760.4684-0.06490.29415.7295-7.7479156.5714
47.1545-3.33441.87364.645-0.11952.6364-0.55340.51020.7009-0.1240.1929-0.11960.11830.01470.29190.2613-0.0835-0.03140.37920.11460.375637.987719.0228164.0157
54.7567-1.21520.60510.5239-0.02020.4475-0.51670.37150.5547-0.0704-0.0061-0.0229-0.24590.15180.5370.35-0.0752-0.01010.43420.04780.47440.5219.2571163.9736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:56 )A3 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:162 )A57 - 162
3X-RAY DIFFRACTION3( CHAIN A AND RESID 163:271 )A163 - 271
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1:11 )F1 - 11
5X-RAY DIFFRACTION5( CHAIN G AND RESID 1:11 )G1 - 11

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