[English] 日本語
Yorodumi
- PDB-1yf3: T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making No... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yf3
TitleT4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact
Components
  • 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'
  • 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'
  • DNA adenine methylase
KeywordsTransferase/DNA / T4DAM / METHYLTRANSFERASE / DNA / 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: 2.29 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
DepositionDec 30, 2004Deposition 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 / Item: _software.classification / _software.name
Revision 1.4Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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) Residue 119 were modeled (for both A and B) as Tyr in this structure as the electron density does not support an Asp here. The electron denstiy for B119 fits a Tyr residue perfectly.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'
D: 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'
A: DNA adenine methylase
B: DNA adenine methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9158
Polymers68,9624
Non-polymers9534
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.900, 125.800, 73.200
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA chain , 2 types, 2 molecules CD

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


Mass: 3935.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs
#2: DNA chain 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'


Mass: 4006.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs

-
Protein , 1 types, 2 molecules AB

#3: Protein DNA adenine methylase / / 2.1.1.72 / Deoxyadenosyl-methyltransferase / M.EcoT4Dam


Mass: 30509.988 Da / Num. of mol.: 2
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)

-
Non-polymers , 3 types, 208 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG MME 5000, citrate-phosphate, ammonium sulphate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG MME 500011
2citrate-phosphate11
3ammonium sulphate11
4H2O11
5PEG MME 500012
6H2O12

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 2.29→28 Å / Num. obs: 29474 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.047 / Net I/σ(I): 22.5
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 9.6 / Rsym value: 0.187 / % possible all: 97.3

-
Processing

Software
NameClassification
XDSdata scaling
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q0S

1q0s


Resolution: 2.29→28 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2825 -RANDOM
Rwork0.214 ---
all0.221 28663 --
obs0.221 28663 93.8 %-
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20.55 Å2
2--9.35 Å20 Å2
3----10 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-28 Å
Luzzati sigma a0.34 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.29→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 509 64 204 4804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_deg1.53
LS refinement shellResolution: 2.29→2.37 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.349 237 -
Rwork0.273 --
obs--92.9 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more