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

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Basic information

Entry
Database: PDB / ID: 4rtk
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with SAH 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 / 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-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / : / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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)41,5135
Polymers41,0363
Non-polymers4772
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.331, 63.044, 142.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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DNA chain , 2 types, 2 molecules FG

#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)

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Non-polymers , 3 types, 101 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 16% 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: 1.96→26.222 Å / Num. all: 24335 / Num. obs: 23847 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.4
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2374 / % 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: 1.96→26.2 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1152 4.84 %RANDOM
Rwork0.2103 ---
obs0.211 23812 98.08 %-
all-24335 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 444 32 99 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022558
X-RAY DIFFRACTIONf_angle_d0.63567
X-RAY DIFFRACTIONf_dihedral_angle_d18.275950
X-RAY DIFFRACTIONf_chiral_restr0.027382
X-RAY DIFFRACTIONf_plane_restr0.003386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.04930.29871520.26242813X-RAY DIFFRACTION100
2.0493-2.15730.28151600.25032815X-RAY DIFFRACTION99
2.1573-2.29240.30491460.2442822X-RAY DIFFRACTION99
2.2924-2.46920.27461310.24332826X-RAY DIFFRACTION99
2.4692-2.71750.25891360.23572840X-RAY DIFFRACTION99
2.7175-3.11020.27921410.24892840X-RAY DIFFRACTION98
3.1102-3.91640.19741250.19062860X-RAY DIFFRACTION97
3.9164-26.2240.17731610.1752844X-RAY DIFFRACTION93
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)
12.0857-0.3803-0.31132.0091.2292.49130.0910.1487-0.1481-0.1184-0.03820.34730.1359-0.3891-0.01330.2459-0.0164-0.06080.27780.05110.2913-10.3997-5.203292.3317
21.720.37470.3793.8909-0.63891.83580.1324-0.5490.38990.88280.0070.634-0.3403-0.3391-0.11450.31950.08540.07870.4193-0.03360.3832-10.31939.6717109.8084
31.241-0.16120.22293.8908-0.55781.9252-0.0286-0.0840.01290.10670.11730.164-0.0897-0.1154-0.06990.20120.0338-0.01370.25560.00260.204-3.74967.9284101.53
42.4345-1.18840.94611.2674-0.11862.98340.29630.3382-0.4219-0.3677-0.17140.0620.83250.1154-0.1130.52530.0748-0.0790.3728-0.04180.3928-2.0554-14.537188.0211
53.8776-0.4551-0.08571.6923-0.77122.9430.35850.7655-0.3134-0.5857-0.3529-0.07750.32960.4149-0.02840.47880.12610.01310.4883-0.0240.3381.7529-7.346278.7388
62.4452-0.5643-0.84373.1379-0.06132.05860.43140.9389-0.2171-0.9261-0.30.41440.255-0.4906-0.10020.5810.1129-0.09590.6093-0.07010.3334-6.971-7.062673.6785
74.0065-1.24680.61671.073-0.10821.72-0.49890.19410.62390.05190.2376-0.27990.01090.06440.31490.3558-0.0301-0.01670.41470.02920.474817.789818.072885.2329
81.4316-0.0195-0.67810.75390.0470.5672-0.42070.41960.1132-0.1577-0.0846-0.1762-0.24030.08340.43570.3764-0.0584-0.01490.5090.08030.499820.243218.320585.0819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:68 )A3 - 68
2X-RAY DIFFRACTION2( CHAIN A AND RESID 69:87 )A69 - 87
3X-RAY DIFFRACTION3( CHAIN A AND RESID 88:162 )A88 - 162
4X-RAY DIFFRACTION4( CHAIN A AND RESID 163:180 )A163 - 180
5X-RAY DIFFRACTION5( CHAIN A AND RESID 181:219 )A181 - 219
6X-RAY DIFFRACTION6( CHAIN A AND RESID 220:270 )A220 - 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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