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- PDB-8k0h: Structure of Cas5f-8f -

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Basic information

Entry
Database: PDB / ID: 8k0h
TitleStructure of Cas5f-8f
Components
  • Csy1
  • Csy2
KeywordsRNA BINDING PROTEIN / dimer / complex
Function / homologyCRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / Csy2 / Csy1
Function and homology information
Biological speciesVibrio phage ICP1_2011_A (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.56 Å
AuthorsFeng, Y. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system.
Authors: Zhang, L. / Wang, H. / Zeng, J. / Cao, X. / Gao, Z. / Liu, Z. / Li, F. / Wang, J. / Zhang, Y. / Yang, M. / Feng, Y.
History
DepositionJul 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csy1
B: Csy2


Theoretical massNumber of molelcules
Total (without water)47,8112
Polymers47,8112
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-28 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.575, 68.186, 73.631
Angle α, β, γ (deg.)90.00, 109.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Csy1 / Cas8f


Mass: 20409.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy1, ICP12011A_088 / Production host: Escherichia coli (E. coli) / References: UniProt: M1R2X3
#2: Protein Csy2 / Cas5f


Mass: 27401.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2011_A (virus) / Gene: csy2, ICP12011A_087 / Production host: Escherichia coli (E. coli) / References: UniProt: M1QWL5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 14740 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 18.3
Reflection shellResolution: 2.56→2.65 Å / Rmerge(I) obs: 0.645 / Num. unique obs: 1351

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.56→46.692 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 741 5.08 %
Rwork0.1918 --
obs0.1941 14734 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→46.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 47 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033211
X-RAY DIFFRACTIONf_angle_d0.7074337
X-RAY DIFFRACTIONf_dihedral_angle_d14.1151182
X-RAY DIFFRACTIONf_chiral_restr0.027479
X-RAY DIFFRACTIONf_plane_restr0.003557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.29091320.23152488X-RAY DIFFRACTION89
2.6512-2.75730.25891470.23392705X-RAY DIFFRACTION98
2.7573-2.88280.29231190.22862698X-RAY DIFFRACTION97
2.8828-3.03470.30061480.22932745X-RAY DIFFRACTION99
3.0347-3.22480.29761750.22112745X-RAY DIFFRACTION99
3.2248-3.47370.2091570.20282708X-RAY DIFFRACTION99
3.4737-3.82320.21031340.18372778X-RAY DIFFRACTION99
3.8232-4.3760.22791650.16462743X-RAY DIFFRACTION99
4.376-5.5120.20791370.16342744X-RAY DIFFRACTION99
5.512-46.6920.19081350.18332735X-RAY DIFFRACTION98

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