[English] 日本語
Yorodumi
- PDB-1a0i: ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITH ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a0i
TitleATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITH ATP
ComponentsDNA LIGASE
KeywordsLIGASE / DNA REPLICATION
Function / homology
Function and homology information


DNA ligation involved in DNA repair / DNA ligase (ATP) / DNA ligase (ATP) activity / double-stranded DNA binding / DNA recombination / DNA replication / ATP binding / metal ion binding
Similarity search - Function
DNA ligase, bacteriophage T7-type / DNA ligase, ATP-dependent, bacteriophage T7-type, C-terminal / DNA ligase C-terminal domain / Dna Ligase; domain 1 - #70 / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central ...DNA ligase, bacteriophage T7-type / DNA ligase, ATP-dependent, bacteriophage T7-type, C-terminal / DNA ligase C-terminal domain / Dna Ligase; domain 1 - #70 / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase/mRNA capping enzyme / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA ligase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsSubramanya, H.S. / Doherty, A.J. / Ashford, S.R. / Wigley, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
Authors: Subramanya, H.S. / Doherty, A.J. / Ashford, S.R. / Wigley, D.B.
History
DepositionDec 1, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3962
Polymers39,8881
Non-polymers5071
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 85.200, 79.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein DNA LIGASE /


Mass: 39888.496 Da / Num. of mol.: 1 / Mutation: M2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: LIG / Plasmid: T7 / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P00969, DNA ligase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.9 / Method: vapor diffusion, hanging drop / Details: Doherty, A.J., (1996) J. Biol. Chem., 271, 11083.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
250 mMBis Tris-HCl1drop
32 mMEDTA1drop
45 mMdithiothreitol1drop
5100 mMBis Tris-HCl1reservoir
6100 mM1reservoirNaCl
712 %(w/v)methoxyPEG50001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 13758 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.114 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→10 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.341 -5 %RANDOM
Rwork0.222 ---
obs0.222 13758 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 31 193 2903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.48 -
Rwork0.338 1456

+
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