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- PDB-5liq: The structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking en... -

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Basic information

Entry
Database: PDB / ID: 5liq
TitleThe structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking endonuclease at 0.185 nm resolution .
ComponentsNicking endonuclease N.BspD6I
KeywordsHYDROLASE / NICKING ENDONUCLEASE / RESTRICTION ENZYME HYDROLASE ACTIVITY'S MUTANT
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 / Nicking endonuclease N.BspD6I
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKachalova, G.S. / Artyukh, R.I. / Perevyazova, T.A. / Yunusova, A.K. / Popov, A.N. / Bartunik, H.D. / Zheleznaya, L.A.
CitationJournal: To Be Published
Title: Structural features of Cysteine residues mutation of the nicking endonuclease Nt.BspD6I.
Authors: Kachalova, G.S. / Yunusova, A.K. / Popov, A.N. / Artyukh, R.I. / Perevyazova, T.A. / Bartunik, H.D. / Zheleznaya, L.A.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicking endonuclease N.BspD6I
B: Nicking endonuclease N.BspD6I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70917
Polymers143,3082
Non-polymers1,40215
Water5,314295
1
A: Nicking endonuclease N.BspD6I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,58611
Polymers71,6541
Non-polymers93210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicking endonuclease N.BspD6I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1236
Polymers71,6541
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.204, 92.485, 113.808
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nicking endonuclease N.BspD6I


Mass: 71653.891 Da / Num. of mol.: 2 / Mutation: C160S ; C508S; C578S
Source method: isolated from a genetically manipulated source
Details: three mutations : C160S C508S C578S / Source: (gene. exp.) Bacillus sp. (bacteria) / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GCA3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: long needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 16% PEG 8000 40MM POTASSIUM PHOSPHATE 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2016 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.85→109.6 Å / Num. obs: 129563 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 34.15 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EWF

2ewf


Resolution: 1.85→19.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.044 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25143 6247 4.8 %RANDOM
Rwork0.20915 ---
obs0.21116 122837 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.377 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å2-0 Å21.1 Å2
2---0.63 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9671 0 83 295 10049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.96713563
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39451196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84124.882508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5281556
X-RAY DIFFRACTIONr_chiral_restr0.1430.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217478
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6734.4734718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.8476.6665906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4345.0435352
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.79442.5244067
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 434 -
Rwork0.36 8995 -
obs--99.51 %

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