[English] 日本語
Yorodumi
- PDB-7cpw: Complex structure of DNA with self-catalyzed depurination activity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cpw
TitleComplex structure of DNA with self-catalyzed depurination activity
Components
  • DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')
  • DNA polymerase beta-like protein
KeywordsTRANSFERASE/DNA / DNAzyme / depurination / GAGA motif / DNA / TRANSFERASE-DNA complex
Function / homology
Function and homology information


base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.849 Å
AuthorsGan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870721 China
CitationJournal: Methods Mol.Biol. / Year: 2022
Title: Crystallization and Structural Determination of 8-17 DNAzyme.
Authors: Liu, H. / Mao, S. / Sheng, J. / Gan, J.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase beta-like protein
B: DNA polymerase beta-like protein
a: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')
b: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)53,5874
Polymers53,5874
Non-polymers00
Water1448
1
A: DNA polymerase beta-like protein
a: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')

A: DNA polymerase beta-like protein
a: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)53,5874
Polymers53,5874
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
2
B: DNA polymerase beta-like protein
b: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')

B: DNA polymerase beta-like protein
b: DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)53,5874
Polymers53,5874
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_595x,-y+4,-z1
Unit cell
Length a, b, c (Å)51.049, 64.544, 172.673
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain a
21chain b
12(chain A and (resid 0 through 82 or resid 84 through 174))
22(chain B and (resid 0 through 82 or resid 84...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DCDCDGDGchain aaC1 - 201 - 20
211DCDCDGDGchain bbD1 - 201 - 20
112GLYGLYGLYGLY(chain A and (resid 0 through 82 or resid 84 through 174))AA0 - 824 - 86
122ARGARGLEULEU(chain A and (resid 0 through 82 or resid 84 through 174))AA84 - 17488 - 178
212GLYGLYGLYGLY(chain B and (resid 0 through 82 or resid 84...BB0 - 824 - 86
222ARGARGARGARG(chain B and (resid 0 through 82 or resid 84...BB84 - 16888 - 172
232GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
242GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
252GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
262GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
272GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
282GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
292GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
2102GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178
2112GLYGLYLEULEU(chain B and (resid 0 through 82 or resid 84...BB0 - 1744 - 178

NCS ensembles :
ID
1
2

-
Components

#1: Protein DNA polymerase beta-like protein / PO174L / PolX


Mass: 20609.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: O174L / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1E3N6
#2: DNA chain DNA (5'-D(*CP*GP*TP*GP*AP*TP*CP*GP*GP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*G)-3')


Mass: 6184.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.74 Å3/Da / Density % sol: 55 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, sodium chloride, Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.849→30 Å / Num. obs: 13544 / % possible obs: 97.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 57.9 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.136 / Net I/σ(I): 16
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1282 / CC1/2: 0.33 / CC star: 0.71 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HRB

5hrb


Resolution: 2.849→29.356 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 661 4.89 %
Rwork0.1958 12861 -
obs0.1987 13522 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.33 Å2 / Biso mean: 65.3719 Å2 / Biso min: 35.8 Å2
Refinement stepCycle: final / Resolution: 2.849→29.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 822 0 8 3667
Biso mean---50.23 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043818
X-RAY DIFFRACTIONf_angle_d0.7815320
X-RAY DIFFRACTIONf_chiral_restr0.048615
X-RAY DIFFRACTIONf_plane_restr0.004516
X-RAY DIFFRACTIONf_dihedral_angle_d13.6922538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11a392X-RAY DIFFRACTION10.846TORSIONAL
12b392X-RAY DIFFRACTION10.846TORSIONAL
21A1630X-RAY DIFFRACTION10.846TORSIONAL
22B1630X-RAY DIFFRACTION10.846TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8495-3.06930.35681060.2804235791
3.0693-3.37780.30721410.2276252597
3.3778-3.86560.24881350.1873257998
3.8656-4.86660.23321360.1726261598
4.8666-29.3560.23571430.1858278599
Refinement TLS params.Method: refined / Origin x: -5.9695 Å / Origin y: 92.4991 Å / Origin z: 21.6173 Å
111213212223313233
T0.4491 Å2-0.194 Å2-0.138 Å2-0.4212 Å20.1719 Å2--0.512 Å2
L0.4281 °2-0.2891 °2-0.1119 °2-0.3748 °20.1097 °2--0.1773 °2
S0.0251 Å °-0.014 Å °0.0926 Å °-0.0786 Å °0.0177 Å °-0.0962 Å °-0.023 Å °0.0062 Å °-0.0257 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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