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- PDB-6qnz: Crystal structure of the site-specific DNA nickase N.BspD6I E418A... -

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Basic information

Entry
Database: PDB / ID: 6qnz
TitleCrystal structure of the site-specific DNA nickase N.BspD6I E418A Mutant
ComponentsHeterodimeric restriction endonuclease R.BspD6I large subunit
KeywordsHYDROLASE / Nickase / endonuclease / Nt.BspD6I / nicking / DNA
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #310 / Restriction Endonuclease - #50 / Restriction endonuclease, type II, AlwI / AlwI restriction endonuclease / Restriction Endonuclease / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Heterodimeric restriction endonuclease R.BspD6I large subunit
Similarity search - Component
Biological speciesBacillus sp. D6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsArtyukh, R.I. / Kachalova, G.S. / Yunusova, A.K. / Gabdulkhakov, A.G. / Fatkhullin, B.F. / Atanasov, B.P. / Perevyazova, T.A. / Popov, A.N. / Zheleznaya, L.A.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: The key role of E418 carboxyl group in the formation of Nt.BspD6I nickase active site: Structural and functional properties of Nt.BspD6I E418A mutant.
Authors: Artyukh, R.I. / Kachalova, G.S. / Yunusova, A.K. / Fatkhullin, B.F. / Atanasov, B.P. / Perevyazova, T.A. / Popov, A.N. / Gabdulkhakov, A.G. / Zheleznaya, L.A.
History
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 24, 2024Group: 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 / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterodimeric restriction endonuclease R.BspD6I large subunit
B: Heterodimeric restriction endonuclease R.BspD6I large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2899
Polymers141,6302
Non-polymers6597
Water1629
1
A: Heterodimeric restriction endonuclease R.BspD6I large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1895
Polymers70,8151
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterodimeric restriction endonuclease R.BspD6I large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1004
Polymers70,8151
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.430, 92.250, 113.800
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heterodimeric restriction endonuclease R.BspD6I large subunit


Mass: 70815.148 Da / Num. of mol.: 2 / Mutation: E418A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. D6 (bacteria) / Gene: bspD6R1 / Production host: Escherichia coli (E. coli) / Strain (production host): NovaBlue(DE3) / References: UniProt: A3FEV7
#2: 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
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.45→47.11 Å / Num. obs: 49355 / % possible obs: 87.8 % / Redundancy: 2.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.52
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 5127 / CC1/2: 0.75 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EWF

2ewf


Resolution: 2.45→47.11 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2459 4.99 %
Rwork0.2309 --
obs0.2315 49261 87.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9452 0 37 9 9498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049686
X-RAY DIFFRACTIONf_angle_d0.63113041
X-RAY DIFFRACTIONf_dihedral_angle_d17.7613725
X-RAY DIFFRACTIONf_chiral_restr0.0431416
X-RAY DIFFRACTIONf_plane_restr0.0041665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.49710.31671430.32792715X-RAY DIFFRACTION92
2.4971-2.54810.32911440.31452736X-RAY DIFFRACTION92
2.5481-2.60350.331380.30632616X-RAY DIFFRACTION91
2.6035-2.6640.36131410.30382672X-RAY DIFFRACTION90
2.664-2.73070.33291380.30452624X-RAY DIFFRACTION89
2.7307-2.80450.34841360.27742590X-RAY DIFFRACTION89
2.8045-2.8870.30191390.27992679X-RAY DIFFRACTION90
2.887-2.98020.26241400.27222649X-RAY DIFFRACTION90
2.9802-3.08670.3411370.27872622X-RAY DIFFRACTION89
3.0867-3.21020.28231380.26482639X-RAY DIFFRACTION90
3.2102-3.35630.27691380.27672638X-RAY DIFFRACTION89
3.3563-3.53320.31350.24462556X-RAY DIFFRACTION86
3.5332-3.75450.19091350.23142552X-RAY DIFFRACTION86
3.7545-4.04420.20411350.22092586X-RAY DIFFRACTION87
4.0442-4.45090.23211340.19972544X-RAY DIFFRACTION86
4.4509-5.09430.20391310.18912490X-RAY DIFFRACTION83
5.0943-6.41570.22581300.22022472X-RAY DIFFRACTION83
6.4157-47.12320.18531270.17842422X-RAY DIFFRACTION79

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