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- PDB-5liz: The structure of Nt.BspD6I nicking endonuclease with all cysteine... -

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Basic information

Entry
Database: PDB / ID: 5liz
TitleThe structure of Nt.BspD6I nicking endonuclease with all cysteines mutated by serine residues at 0.19 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: 1.93 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7332
Polymers71,6381
Non-polymers951
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-6 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.867, 93.059, 76.580
Angle α, β, γ (deg.)90.00, 112.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nicking endonuclease N.BspD6I


Mass: 71637.820 Da / Num. of mol.: 1 / Mutation: C11S C160S C508S C578S
Source method: isolated from a genetically manipulated source
Details: four mutations C11S C160S C508S C578S / Source: (gene. exp.) Bacillus sp. (bacteria) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GCA3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.86 Å3/Da / Density % sol: 57 %
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: 0.96862 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.93→47.45 Å / Num. obs: 57969 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.1
Reflection shellResolution: 1.93→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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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: 1.93→19.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.08 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.23927 2837 4.9 %RANDOM
Rwork0.20712 ---
obs0.20863 54989 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.405 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å2-0.19 Å2
2--1 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.93→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4837 0 5 155 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9626761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2524.981257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85315977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1351528
X-RAY DIFFRACTIONr_chiral_restr0.1470.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213756
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_it4.3253.6642362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9295.4512956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8734.0972650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.07334.44622400
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: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 223 -
Rwork0.311 4007 -
obs--99.72 %

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