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- PDB-8wth: Crystal structure of Cas3-HD -

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Basic information

Entry
Database: PDB / ID: 8wth
TitleCrystal structure of Cas3-HD
ComponentsHD Cas3-type domain-containing protein
KeywordsMETAL BINDING PROTEIN / Cas3-HD is a di-ion dependent ssDNA nuclease
Function / homologyCRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / HD Cas3-type domain profile. / HD domain / HD domain / defense response to virus / hydrolase activity / metal ion binding / HD Cas3-type domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 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 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HD Cas3-type domain-containing protein


Theoretical massNumber of molelcules
Total (without water)22,2421
Polymers22,2421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.656, 41.706, 47.983
Angle α, β, γ (deg.)90.000, 98.881, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein HD Cas3-type domain-containing protein


Mass: 22241.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH0916 / Production host: Escherichia coli (E. coli) / References: UniProt: O58617
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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 30% PEG8000, 0. 2 M Ammonium sulfate, and 0.1 M Tris at a pH of 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: MAR CCD 130 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: 3.45→29 Å / Num. obs: 2998 / % possible obs: 99.3 % / Redundancy: 3 % / Biso Wilson estimate: 52.04 Å2 / CC1/2: 0.78 / Net I/σ(I): 6
Reflection shellResolution: 3.45→3.57 Å / Num. unique obs: 299 / CC1/2: 0.78

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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: 3.45→25.8 Å / SU ML: 0.4088 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2946 143 4.77 %
Rwork0.2607 2853 -
obs0.2623 2996 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.69 Å2
Refinement stepCycle: LAST / Resolution: 3.45→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 0 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281567
X-RAY DIFFRACTIONf_angle_d0.68562108
X-RAY DIFFRACTIONf_chiral_restr0.0425231
X-RAY DIFFRACTIONf_plane_restr0.0049265
X-RAY DIFFRACTIONf_dihedral_angle_d5.2813204
LS refinement shellResolution: 3.45→25.8 Å
RfactorNum. reflection% reflection
Rfree0.2946 143 -
Rwork0.2607 2853 -
obs--99.6 %

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