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- PDB-6jhz: Crystal structure of cas2 -

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Basic information

Entry
Database: PDB / ID: 6jhz
TitleCrystal structure of cas2
Components
  • 5-mer peptide
  • CRISPR-associated endoribonuclease Cas2
KeywordsRNA BINDING PROTEIN / crispr / 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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.999 Å
AuthorsBi, M. / Mo, X. / Wang, C. / Yuan, A.Y.
CitationJournal: To be published
Title: Structural insight into endonuclease CRISPR-associated Cas2 protein
Authors: Bi, M. / Mo, X. / Wang, C. / Yuan, A.Y.
History
DepositionFeb 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2
Q: 5-mer peptide


Theoretical massNumber of molelcules
Total (without water)22,0393
Polymers22,0393
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
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.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 10867.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) (bacteria)
Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: cas2, TDE_0329 / Production host: Escherichia coli (E. coli)
References: UniProt: Q73QW4, Hydrolases; Acting on ester bonds
#2: Protein/peptide 5-mer peptide


Mass: 303.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, pH8.5, 2M Ammonium sulfate

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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 165 mm / Detector: CCD / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.999→19.746 Å / Num. obs: 13958 / % possible obs: 99.19 % / Redundancy: 7.5 % / Net I/σ(I): 13.5
Reflection shellResolution: 1.999→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementResolution: 1.999→19.746 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.2322 960 7.53 %
Rwork0.1951 --
obs0.1979 12757 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.999→19.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 0 153 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071555
X-RAY DIFFRACTIONf_angle_d0.8612091
X-RAY DIFFRACTIONf_dihedral_angle_d2.433959
X-RAY DIFFRACTIONf_chiral_restr0.057242
X-RAY DIFFRACTIONf_plane_restr0.005259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9991-2.10440.25261360.18731594X-RAY DIFFRACTION96
2.1044-2.2360.23981340.18451662X-RAY DIFFRACTION100
2.236-2.40840.22681440.19241653X-RAY DIFFRACTION100
2.4084-2.65020.27181290.20911685X-RAY DIFFRACTION100
2.6502-3.03260.23341300.21181685X-RAY DIFFRACTION100
3.0326-3.81620.24551550.19161712X-RAY DIFFRACTION100
3.8162-19.74710.19771320.19051806X-RAY DIFFRACTION99

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