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- PDB-7cpw: Complex structure of DNA with self-catalyzed depurination activity -

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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


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, thumb domain superfamily / DNA polymerase beta thumb / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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

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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

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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

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