[English] 日本語
Yorodumi
- PDB-6iml: The crystal structure of AsfvLIG:CT1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iml
TitleThe crystal structure of AsfvLIG:CT1 complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')
  • DNA ligase
KeywordsLIGASE/DNA / The crysatl structure of AsfvLIG with C:G complex / LIGASE-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding
Similarity search - Function
ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, Y.Q. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues.
Authors: Chen, Y. / Liu, H. / Yang, C. / Gao, Y. / Yu, X. / Chen, X. / Cui, R. / Zheng, L. / Li, S. / Li, X. / Ma, J. / Huang, Z. / Li, J. / Gan, J.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA ligase
C: DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')
D: DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*T)-3')
E: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)61,6724
Polymers61,6724
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-38 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.244, 53.735, 76.232
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DNA ligase / / NP419L / PNP419L


Mass: 48233.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: NP419L / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1E0U0
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*CP*CP*GP*CP*AP*TP*CP*CP*CP*GP*GP*A)-3')


Mass: 6643.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*CP*GP*GP*GP*AP*TP*GP*CP*GP*T)-3')


Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*AP*CP*TP*GP*G)-3')


Mass: 3101.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 15% w/v PEG 10000, 0.1 M Ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 23122 / % possible obs: 95.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 2021 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YMJ

6ymj


Resolution: 2.35→29.884 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65
RfactorNum. reflection% reflection
Rfree0.2678 1177 5.1 %
Rwork0.2192 --
obs0.2217 23094 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 895 0 67 4102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034217
X-RAY DIFFRACTIONf_angle_d0.495903
X-RAY DIFFRACTIONf_dihedral_angle_d17.6772341
X-RAY DIFFRACTIONf_chiral_restr0.04663
X-RAY DIFFRACTIONf_plane_restr0.003601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3463-2.45310.37941120.31582270X-RAY DIFFRACTION79
2.4531-2.58230.36411480.31712606X-RAY DIFFRACTION91
2.5823-2.7440.34661610.29932728X-RAY DIFFRACTION96
2.744-2.95570.36561650.28912780X-RAY DIFFRACTION98
2.9557-3.25280.29751410.24452823X-RAY DIFFRACTION98
3.2528-3.72270.26251490.20012876X-RAY DIFFRACTION99
3.7227-4.68730.22721330.1772902X-RAY DIFFRACTION99
4.6873-29.88620.20521680.17842932X-RAY DIFFRACTION99

+
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