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- PDB-8wtk: Crystal structure of Cas3-DExD+MG -

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Basic information

Entry
Database: PDB / ID: 8wtk
TitleCrystal structure of Cas3-DExD+MG
ComponentsCRISPR-associated helicase Cas3
KeywordsMETAL BINDING PROTEIN / Cas3-DExD is a di-ion dependent ssDNA nuclease
Function / homology
Function and homology information


catalytic activity, acting on DNA / helicase activity / defense response to virus / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
Helicase Cas3, CRISPR-associated, core / : / CRISPR-associated nuclease/helicase Cas3, C-terminal / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CRISPR-associated helicase Cas3
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.08 Å
AuthorsMo, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071476 China
CitationJournal: To be published
Title: Structural insight into dynamic characteristic of the polymerized forms of kinetoplastid membrane protein-11
Authors: Mo, X.
History
DepositionOct 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated helicase Cas3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3712
Polymers60,3471
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.756, 114.756, 119.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein CRISPR-associated helicase Cas3


Mass: 60346.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: cas3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832T690
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 295.15 K / Method: evaporation
Details: 15% PEG3350, 10% glycerol, and 0.1 M Tris at a pH of 6.4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→29 Å / Num. obs: 17162 / % possible obs: 99.54 % / Redundancy: 5 % / Biso Wilson estimate: 97.66 Å2 / CC1/2: 0.85 / Net I/σ(I): 6
Reflection shellResolution: 3.08→3.19 Å / Num. unique obs: 1668 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.08→28.98 Å / SU ML: 0.4632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2695 1712 9.98 %
Rwork0.2241 15449 -
obs0.2286 17161 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.94 Å2
Refinement stepCycle: LAST / Resolution: 3.08→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 1 0 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244112
X-RAY DIFFRACTIONf_angle_d0.60325545
X-RAY DIFFRACTIONf_chiral_restr0.0454628
X-RAY DIFFRACTIONf_plane_restr0.004704
X-RAY DIFFRACTIONf_dihedral_angle_d6.277539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.170.47111390.33361234X-RAY DIFFRACTION97.65
3.17-3.270.41051420.30771269X-RAY DIFFRACTION99.58
3.28-3.390.34851370.27761261X-RAY DIFFRACTION99.79
3.39-3.530.33221420.25541273X-RAY DIFFRACTION99.93
3.53-3.690.36481470.26961273X-RAY DIFFRACTION99.72
3.69-3.880.30141430.24731276X-RAY DIFFRACTION99.86
3.88-4.120.26951420.24741277X-RAY DIFFRACTION99.93
4.12-4.440.24451420.2091284X-RAY DIFFRACTION99.86
4.44-4.890.21591360.18191305X-RAY DIFFRACTION100
4.89-5.590.25831410.20791294X-RAY DIFFRACTION100
5.59-7.020.25741440.24221327X-RAY DIFFRACTION100
7.03-28.980.2341570.19451376X-RAY DIFFRACTION99.93

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