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

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Basic information

Entry
Database: PDB / ID: 4rtr
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTTTA )
Components
  • DNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*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
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / : / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 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(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')
G: DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0504
Polymers41,6523
Non-polymers3981
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.660, 62.922, 136.272
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(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')


Mass: 3629.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*G)-3')


Mass: 3691.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 4000, 80mM Magnesium acetate, 50mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING 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: Jun 14, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. all: 14421 / Num. obs: 14421 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1360 / % possible all: 90.5

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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: 2.393→29.959 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 720 5 %RANDOM
Rwork0.1767 ---
obs0.1792 14395 93.22 %-
all-14395 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.393→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 468 27 105 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032599
X-RAY DIFFRACTIONf_angle_d0.5813622
X-RAY DIFFRACTIONf_dihedral_angle_d18.55981
X-RAY DIFFRACTIONf_chiral_restr0.024384
X-RAY DIFFRACTIONf_plane_restr0.003389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.393-2.5780.24671440.22152614X-RAY DIFFRACTION91
2.578-2.83720.27361440.21572697X-RAY DIFFRACTION93
2.8372-3.24740.2561440.20012795X-RAY DIFFRACTION97
3.2474-4.08970.21331440.15622816X-RAY DIFFRACTION96
4.0897-29.9610.20141440.15862753X-RAY DIFFRACTION89
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)
10.33650.6274-0.51691.1845-1.01220.9121-0.40821.08560.0588-0.82560.4742-0.2244-0.1987-0.4326-0.04540.4996-0.00840.05730.6010.07020.3841-11.8907-34.2679152.4719
20.85920.2962-0.13913.1916-0.56811.57850.00970.0659-0.06510.1334-0.0302-0.236-0.04250.12310.02460.18350.0254-0.00580.201-0.00750.2197-16.7183-34.0218162.2384
32.33210.18420.17682.5391-0.74183.2370.04270.3433-0.0133-0.44760.11180.0749-0.1506-0.0532-0.15020.40830.0212-0.00440.37220.03490.2393-24.0137-21.3509141.9362
44.4073-0.17160.81411.73820.05112.1971-0.57730.7662-0.6171-0.34210.31380.49120.1296-0.05560.1590.3775-0.0858-0.0590.6473-0.17060.5878-44.5105-49.1903150.6147
51.8962-0.44920.63170.372-0.40070.4554-0.5411.7217-0.3399-0.11970.11810.1128-0.01440.23380.3390.2765-0.05790.00320.6677-0.15210.489-46.5484-49.4531151.1816
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 18:162 )A18 - 162
3X-RAY DIFFRACTION3( CHAIN A AND RESID 163:272 )A163 - 272
4X-RAY DIFFRACTION4( CHAIN F AND RESID 2:12 )F2 - 12
5X-RAY DIFFRACTION5( CHAIN G AND RESID 1:12 )G1 - 12

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