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

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Basic information

Entry
Database: PDB / ID: 4rtp
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet 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-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: 2.39 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)41,4344
Polymers41,0353
Non-polymers3981
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.817, 63.225, 144.102
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-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.: 25 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% 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: 2.39→34.8 Å / Num. all: 13573 / Num. obs: 13573 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.3
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1312 / % possible all: 99.8

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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: 2.39→34.759 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 684 5.06 %RANDOM
Rwork0.2165 ---
obs0.2182 13526 99.36 %-
all-13526 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→34.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 445 27 25 2433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022523
X-RAY DIFFRACTIONf_angle_d0.5453528
X-RAY DIFFRACTIONf_dihedral_angle_d18.04920
X-RAY DIFFRACTIONf_chiral_restr0.024382
X-RAY DIFFRACTIONf_plane_restr0.003380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.57450.32291280.25512530X-RAY DIFFRACTION100
2.5745-2.83350.27911390.27422512X-RAY DIFFRACTION100
2.8335-3.24320.30161490.25062536X-RAY DIFFRACTION100
3.2432-4.08510.2421220.19962590X-RAY DIFFRACTION100
4.0851-34.76310.21751460.19812674X-RAY DIFFRACTION98
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)
14.01952.41353.47851.60412.17662.9533-0.33380.99830.1085-0.3290.18170.99180.3062-0.01460.12850.52540.0367-0.07040.60070.06170.6244-13.24323.223991.8708
23.4582-1.1216-0.7285.02880.80934.68510.27010.2842-0.8442-0.58480.04940.98230.4505-0.6989-0.28610.4408-0.0446-0.17330.35780.0590.6142-9.3548-7.321194.4852
36.48052.5017-0.62146.2796-1.24936.74690.0058-1.11120.36261.53840.00370.8017-0.2368-0.76240.11740.39480.08050.07280.5854-0.00750.4155-10.291210.2795111.1808
46.60910.0377-2.42415.5004-1.86435.5449-0.0358-0.23460.45580.41930.125-0.1538-0.32270.1338-0.09110.24530.0386-0.02510.248-0.03940.3247-0.255712.213104.0441
54.96411.0199-1.65316.0121-1.09854.453-0.0804-0.15270.64550.30110.22870.0642-0.5269-0.3012-0.21340.39930.0641-0.04230.26760.00940.2601-3.236314.503199.6244
66.8441-3.16310.54129.06232.22144.69740.0545-0.617-1.38620.489-0.0261.58770.6492-0.622-0.03380.3835-0.107-0.05570.49250.12450.5718-11.9402-5.3583103.0917
75.112-1.53520.64942.68221.17364.91340.3920.82-0.6994-0.7492-0.33530.20020.85270.4293-0.13050.7270.1816-0.08580.6336-0.14580.5065-0.9195-9.987183.4524
81.0218-0.0865-1.27642.00590.90031.85470.33260.6635-0.2376-1.2095-0.37480.54120.9107-0.28420.08871.30760.4899-0.18851.2669-0.20060.5144-5.4756-6.296571.8048
95.4335-3.9621-0.36549.00250.89892.67980.67540.8155-0.08531.0053-0.6363-0.61860.4369-0.20580.0830.78360.1049-0.31230.9385-0.17030.7124-10.0183-5.213275.5983
102.49680.2524-1.98762.3336-0.54182.6173-0.42251.27380.7669-0.51940.0259-0.36630.06270.0430.36740.4738-0.04730.08520.81740.190.770119.831818.707285.9639
112.2431-2.83750.26814.7734-1.25164.2346-0.04920.73970.9331-0.69580.1145-0.6654-0.00340.05020.09140.4834-0.09890.07520.76380.07740.759417.001918.555586.1399
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 69:87 )A69 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:126 )A88 - 126
5X-RAY DIFFRACTION5( CHAIN A AND RESID 127:144 )A127 - 144
6X-RAY DIFFRACTION6( CHAIN A AND RESID 145:162 )A145 - 162
7X-RAY DIFFRACTION7( CHAIN A AND RESID 163:228 )A163 - 228
8X-RAY DIFFRACTION8( CHAIN A AND RESID 229:245 )A229 - 245
9X-RAY DIFFRACTION9( CHAIN A AND RESID 246:270 )A246 - 270
10X-RAY DIFFRACTION10( CHAIN F AND RESID 1:11 )F1 - 11
11X-RAY DIFFRACTION11( CHAIN G AND RESID 1:11 )G1 - 11

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