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- PDB-1yfl: T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showi... -

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Basic information

Entry
Database: PDB / ID: 1yfl
TitleT4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base
Components
  • 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
  • DNA adenine methylase
KeywordsTRANSFERASE/DNA / T4DAM / METHYLTRANSFERASE / DNA / PROTEIN-DNA COMPLEX / BASE-FLIPPING / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


restriction-modification system evasion by virus / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / nucleic acid binding / DNA replication
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine modification methylase, M.EcoRV-type / 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 ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / Adenine modification methylase, M.EcoRV-type / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / DNA (> 10) / DNA / DNA adenine methylase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 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 3, 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: Non-polymer description / 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 1.5Jul 22, 2020Group: Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.propeller ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.y_displacement
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

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Assembly

Deposited unit
F: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
G: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
H: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
I: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
A: DNA adenine methylase
B: DNA adenine methylase
D: DNA adenine methylase
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,96612
Polymers141,4408
Non-polymers1,5264
Water362
1
F: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
G: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
A: DNA adenine methylase
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4836
Polymers70,7204
Non-polymers7632
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
I: 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'
D: DNA adenine methylase
E: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4836
Polymers70,7204
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)87.871, 117.648, 87.865
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 4898.192 Da / Num. of mol.: 4 / 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (bacteriophage)
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)
#3: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.15 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, MES, ammonium acetate, CaCl2, glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2MES11
3ammonium acetate11
4CaCl211
5glycerol11
6H2O11
7PEG 600012
8MES12
9ammonium acetate12
10CaCl212

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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: Jun 6, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→30 Å / Num. obs: 33149 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 54.4 Å2 / Rsym value: 0.081 / Net I/σ(I): 18.7
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 3302 / Rsym value: 0.314 / % 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
Resolution: 3.09→29.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal of T4Dam-sinefungin-16mer DNA can also be indexed in the space group P43, with the same cell dimensions but two protein molecules and two half DNA molecules in the asymmetric ...Details: The crystal of T4Dam-sinefungin-16mer DNA can also be indexed in the space group P43, with the same cell dimensions but two protein molecules and two half DNA molecules in the asymmetric unit. The DNA axis is in parallel with the crystallographic z-axis (a 4-fold screw axis). To have a complete DNA molecule, we indexed the diffraction data in a lower symmetry space group P21. The two protein molecules along the DNA axis were constrained during the refinement by non-crystallographic 4-fold screw symmetry.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1595 -RANDOM
Rwork0.214 ---
all0.217 32163 --
obs0.217 32163 97.9 %-
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.84 Å20 Å20 Å2
2---19.47 Å20 Å2
3---10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-30 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 3.09→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7953 1316 108 2 9379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.09
LS refinement shellResolution: 3.09→3.2 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.392 141 -
Rwork0.362 --
obs--92 %

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