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- PDB-8zns: Type I-C CRISPR-associated protein, Cas3 -

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Basic information

Entry
Database: PDB / ID: 8zns
TitleType I-C CRISPR-associated protein, Cas3
ComponentsCRISPR-associated endonuclease Cas3-HD
KeywordsIMMUNE SYSTEM / Cas3 / CRISPR-Cas system / genome editing / nuclease/helicase / DNA Binding protein
Function / homology
Function and homology information


endonuclease activity / defense response to virus / nucleic acid binding / Hydrolases; Acting on ester bonds / ATP binding / metal ion binding
Similarity search - Function
Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...Helicase Cas3, CRISPR-associated, core / Cas3, HD domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / CRISPR-associated endonuclease Cas3-HD
Similarity search - Component
Biological speciesNeisseria lactamica ATCC 23970 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKim, D.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of Cas3 activation in type I-C CRISPR-Cas system.
Authors: Kim, D.Y. / Lee, S.Y. / Ha, H.J. / Park, H.H.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas3-HD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4273
Polymers96,3161
Non-polymers1122
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-29 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.970, 73.330, 104.420
Angle α, β, γ (deg.)90.000, 99.750, 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 CRISPR-associated endonuclease Cas3-HD


Mass: 96315.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria lactamica ATCC 23970 (bacteria)
Gene: NEILACOT_03977 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D0W8X3, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG 8000, 0.1M Na/K phosphate pH 6.2, 0.2M NaCl

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→29.09 Å / Num. obs: 49372 / % possible obs: 99.88 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.84
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 4905 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→29.09 Å / SU ML: 0.2793 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 2467 5 %
Rwork0.1946 46890 -
obs0.1972 49357 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.41 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 2 351 6569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096358
X-RAY DIFFRACTIONf_angle_d0.99468602
X-RAY DIFFRACTIONf_chiral_restr0.053937
X-RAY DIFFRACTIONf_plane_restr0.00941122
X-RAY DIFFRACTIONf_dihedral_angle_d5.9144842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.210.33091350.27932570X-RAY DIFFRACTION99.89
2.21-2.260.39141380.2842607X-RAY DIFFRACTION99.89
2.26-2.310.34241360.2762580X-RAY DIFFRACTION99.93
2.31-2.360.31211360.25632590X-RAY DIFFRACTION99.89
2.36-2.420.29681370.23922609X-RAY DIFFRACTION99.96
2.42-2.480.33761350.24442567X-RAY DIFFRACTION99.96
2.48-2.560.26161370.23082598X-RAY DIFFRACTION99.96
2.56-2.640.27411350.22052588X-RAY DIFFRACTION99.82
2.64-2.730.26121380.21562606X-RAY DIFFRACTION100
2.73-2.840.26871360.21592590X-RAY DIFFRACTION100
2.84-2.970.28281370.20422608X-RAY DIFFRACTION99.96
2.97-3.130.25461370.20112600X-RAY DIFFRACTION100
3.13-3.320.27451370.20332602X-RAY DIFFRACTION99.89
3.32-3.580.24091370.18312613X-RAY DIFFRACTION100
3.58-3.940.22241380.17252617X-RAY DIFFRACTION100
3.94-4.510.18171390.15232630X-RAY DIFFRACTION99.96
4.51-5.670.21981380.1652627X-RAY DIFFRACTION99.96
5.68-29.090.22961410.17962688X-RAY DIFFRACTION99.93

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