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- PDB-8ia4: Crystal structure of Cas2 in complex with AcrVA5-peptide -

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Basic information

Entry
Database: PDB / ID: 8ia4
TitleCrystal structure of Cas2 in complex with AcrVA5-peptide
Components
  • CRISPR-associated endoribonuclease Cas2
  • peptide
KeywordsGENE REGULATION / CRISPR-Cas / integration / Cas2
Function / homologyCRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding / CRISPR-associated endoribonuclease Cas2
Function and homology information
Biological speciesTreponema denticola (bacteria)
Moraxella bovoculi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMo, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071476 China
CitationJournal: Nat Commun / Year: 2024
Title: Insights into the inhibition of protospacer integration via direct interaction between Cas2 and AcrVA5.
Authors: Bi, M. / Su, W. / Li, J. / Mo, X.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
Q: peptide


Theoretical massNumber of molelcules
Total (without water)24,1073
Polymers24,1073
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.592, 76.391, 88.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 1 - 91 / Label seq-ID: 1 - 91

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and resid 1 through 92)AA
2chain 'B'BB

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 11794.800 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104) (bacteria)
Gene: cas2, TDE_0329 / Production host: Escherichia coli (E. coli)
References: UniProt: Q73QW4, Hydrolases; Acting on ester bonds
#2: Protein/peptide peptide


Mass: 517.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Moraxella bovoculi (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 10% glycerol and 0.1M Tris (pH 6.4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.75 Å / Num. obs: 13960 / % possible obs: 99 % / Redundancy: 7.5 % / Biso Wilson estimate: 18.69 Å2 / CC1/2: 0.9 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 1461 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.75 Å / SU ML: 0.1873 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.317
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 960 7.53 %
Rwork0.1925 11797 -
obs0.1959 12757 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.73 Å2
Refinement stepCycle: LAST / Resolution: 2→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 0 199 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571593
X-RAY DIFFRACTIONf_angle_d0.91082144
X-RAY DIFFRACTIONf_chiral_restr0.0536252
X-RAY DIFFRACTIONf_plane_restr0.0056264
X-RAY DIFFRACTIONf_dihedral_angle_d13.3312207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10.2371360.18161594X-RAY DIFFRACTION96.06
2.1-2.240.24441340.18581662X-RAY DIFFRACTION100
2.24-2.410.25241440.1971653X-RAY DIFFRACTION100
2.41-2.650.25931290.21091685X-RAY DIFFRACTION100
2.65-3.030.26041300.20421685X-RAY DIFFRACTION100
3.03-3.820.25381550.18571712X-RAY DIFFRACTION100
3.82-19.750.19461320.18821806X-RAY DIFFRACTION99.38

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