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- PDB-8wtl: Crystal structure of Cas3-DExD+MG+ATP -

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Basic information

Entry
Database: PDB / ID: 8wtl
TitleCrystal structure of Cas3-DExD+MG+ATP
ComponentsCRISPR-associated helicase Cas3
KeywordsMETAL BINDING PROTEIN / Cas3-DExD proteins belongs to the Superfamily 2 (SF2) helicase family.
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
ADENOSINE-5'-TRIPHOSPHATE / CRISPR-associated helicase Cas3
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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 1.0Oct 30, 2024Provider: repository / Type: Initial release

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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)60,8783
Polymers60,3471
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-12 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.246, 115.246, 119.229
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: 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: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 14.5% PEG3350, 9.8% glycerol, and 0.1 M Tris at a pH of 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.94→29.05 Å / Num. obs: 19850 / % possible obs: 99.53 % / Redundancy: 6.5 % / Biso Wilson estimate: 89.58 Å2 / CC1/2: 0.88 / Net I/σ(I): 7.3
Reflection shellResolution: 2.94→3.045 Å / Num. unique obs: 1939 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→29.05 Å / SU ML: 0.4501 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246 1052 5.3 %
Rwork0.2058 18798 -
obs0.2079 19850 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.13 Å2
Refinement stepCycle: LAST / Resolution: 2.94→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 32 0 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01084145
X-RAY DIFFRACTIONf_angle_d1.46435597
X-RAY DIFFRACTIONf_chiral_restr0.0698632
X-RAY DIFFRACTIONf_plane_restr0.0079705
X-RAY DIFFRACTIONf_dihedral_angle_d10.1239552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.070.38811160.30892320X-RAY DIFFRACTION99.27
3.07-3.230.41241290.28412307X-RAY DIFFRACTION99.59
3.23-3.440.34491400.26742299X-RAY DIFFRACTION99.71
3.44-3.70.28611350.24262339X-RAY DIFFRACTION99.72
3.7-4.070.25481110.20992351X-RAY DIFFRACTION100
4.07-4.660.21231540.17442330X-RAY DIFFRACTION99.88
4.66-5.860.22561490.19412372X-RAY DIFFRACTION100
5.86-29.050.2091180.18342480X-RAY DIFFRACTION99.35

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