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

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Basic information

Entry
Database: PDB / ID: 4rtn
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy 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
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: 2.59 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)41,4204
Polymers41,0353
Non-polymers3841
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.201, 63.477, 144.048
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24% PEG200, 100mM KCl, 10mM MgSO4, 100mM HEPES 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 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: 2.59→29.044 Å / Num. all: 10911 / Num. obs: 10911 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1049 / % possible all: 100

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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: 2.59→29 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 566 5.21 %RANDOM
Rwork0.2051 ---
obs0.2069 10863 99.84 %-
all-10863 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 445 26 34 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032577
X-RAY DIFFRACTIONf_angle_d0.5983603
X-RAY DIFFRACTIONf_dihedral_angle_d17.824945
X-RAY DIFFRACTIONf_chiral_restr0.026390
X-RAY DIFFRACTIONf_plane_restr0.003389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.85320.32161320.27392502X-RAY DIFFRACTION100
2.8532-3.26560.25211380.25392536X-RAY DIFFRACTION100
3.2656-4.11240.24841430.19322563X-RAY DIFFRACTION100
4.1124-29.04540.20591530.1762696X-RAY DIFFRACTION100
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)
10.8686-0.6561-0.19471.47570.08220.69680.14930.1254-0.2419-0.1531-0.02470.43250.158-0.22710.00040.3256-0.0183-0.12430.28960.00840.379-10.3352-5.111993.7697
21.246-0.14890.5541.2852-0.16311.0795-0.0301-0.11390.24310.25110.06290.0485-0.167-0.0666-00.26320.03010.020.2688-0.00750.2463-3.447512.2195104.6998
32.5979-0.6851.24761.0801-0.71761.50870.52990.5545-0.6503-0.4096-0.30360.30830.53880.21610.04190.47090.116-0.1160.3427-0.11960.3341-4.9641-7.722784.0089
40.1072-0.1498-0.0030.459-0.26410.1849-0.62320.88990.5958-0.11220.1216-0.16190.0468-0.0331-0.04560.3778-0.07160.03090.67430.10420.503320.088218.671485.9866
50.2825-0.4791-0.31140.78250.02380.8229-0.23050.8335-0.0889-0.19180.056-0.0891-0.04990.1485-0.00020.4904-0.01880.02230.64920.06210.690317.27818.51186.161
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 69:144 )A69 - 144
3X-RAY DIFFRACTION3( CHAIN A AND RESID 145:270 )A145 - 270
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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