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- PDB-1yfj: T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing S... -

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Basic information

Entry
Database: PDB / ID: 1yfj
TitleT4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact
Components
  • 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
  • DNA adenine methylase
KeywordsTRANSFERASE/DNA / T4DAM / METHYLTRANSFERASE / DNA / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / DNA replication / 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 speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsHorton, J.R. / Liebert, K. / Hattman, S. / Jeltsch, A. / Cheng, X.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2005
Title: Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.
Authors: Horton, J.R. / Liebert, K. / Hattman, S. / Jeltsch, A. / Cheng, X.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Structure of the bacteriophage T4 DNA adenine methyltransferase
Authors: Yang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Cheng, X.
History
DepositionJan 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE 1) Author states that Q139R, Y140F and Q209L reflect conflicts between deposited protein ...SEQUENCE 1) Author states that Q139R, Y140F and Q209L reflect conflicts between deposited protein sequence and translated deposited DNA-->protein sequence. From their electron density, it appears the translated DNA sequence is correct ; 2) It is possible residue 119 could be a Tyr rather than Asp based on some electron density evidence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
2: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
3: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
4: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
5: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
6: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
7: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
8: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
9: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
0: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
A: DNA adenine methylase
B: DNA adenine methylase
C: DNA adenine methylase
D: DNA adenine methylase
E: DNA adenine methylase
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,15028
Polymers228,62116
Non-polymers2,52812
Water6,179343
1
1: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
2: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
A: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1638
Polymers39,6323
Non-polymers5315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
7: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
8: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0525
Polymers39,6323
Non-polymers4202
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
3: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
4: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
C: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0565
Polymers39,6323
Non-polymers4242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
5: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
6: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
D: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,6323
Non-polymers3841
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
9: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
0: 5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0164
Polymers39,6323
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8462
Polymers30,4621
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.200, 133.000, 189.200
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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DNA chain / Protein , 2 types, 16 molecules 1234567890ABCDEF

#1: DNA chain
5'-D(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'


Mass: 4584.985 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs
#2: Protein
DNA adenine methylase / / 2.1.1.72 / Deoxyadenosyl-methyltransferase / M.EcoT4Dam


Mass: 30461.898 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: DAM / Plasmid: pJW2 / Production host: Escherichia coli (E. coli) / Strain (production host): GM 2971
References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific)

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Non-polymers , 4 types, 355 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, ammonium acetate, CaCl2, and ethyleneglycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2MES11
3ammonium acetate11
4CaCl211
5ethyleneglycol11
6H2O11
7PEG 600012
8ammonium acetate12
9CaCl212

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 8, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→35 Å / Num. obs: 78518 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 7801 / Rsym value: 0.323 / % possible all: 100

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q0S

1q0s


Resolution: 2.69→34.78 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3860 -RANDOM
Rwork0.202 ---
all0.206 76093 --
obs0.206 76093 96.8 %-
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2--11.66 Å20 Å2
3----9.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-35 Å
Luzzati sigma a0.33 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.69→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11493 3010 178 327 15008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_deg1.08
LS refinement shellResolution: 2.69→2.79 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.341 352 -
Rwork0.281 --
obs--91.1 %

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