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- PDB-5g4d: Crystal structure of the Cas2 in T.onnurineus -

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Basic information

Entry
Database: PDB / ID: 5g4d
TitleCrystal structure of the Cas2 in T.onnurineus
ComponentsCRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2
KeywordsIMMUNE SYSTEM / CRIPSR-CAS COMPLEX / ADAPTATION
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesTHERMOCOCCUS ONNURINEUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 Å
AuthorsJung, T.Y. / Park, K.H. / Woo, E.J.
CitationJournal: Protein Sci. / Year: 2016
Title: Structural Features of Cas2 from Thermococcus Onnurineus in Crispr-Cas System Type Iv.
Authors: Jung, T. / Park, K. / Yan, A. / Schulga, A. / Deyev, S. / Jung, J. / Woo, E.
History
DepositionMay 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2


Theoretical massNumber of molelcules
Total (without water)10,3771
Polymers10,3771
Non-polymers00
Water1,18966
1
A: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2

A: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2


Theoretical massNumber of molelcules
Total (without water)20,7542
Polymers20,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2730 Å2
ΔGint-11.9 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.515, 32.802, 83.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-2019-

HOH

21A-2065-

HOH

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Components

#1: Protein CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2 / CAS2


Mass: 10377.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOCOCCUS ONNURINEUS (archaea) / References: UniProt: B6YTB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.59 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 9301 / % possible obs: 99.1 % / Observed criterion σ(I): 27.64 / Redundancy: 6.5 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.701→25.753 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 930 10 %
Rwork0.215 --
obs0.2178 9301 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→25.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 0 66 719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006663
X-RAY DIFFRACTIONf_angle_d0.814892
X-RAY DIFFRACTIONf_dihedral_angle_d15.592405
X-RAY DIFFRACTIONf_chiral_restr0.058102
X-RAY DIFFRACTIONf_plane_restr0.004112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.79020.30231270.23951157X-RAY DIFFRACTION100
1.7902-1.90230.29311330.22831184X-RAY DIFFRACTION100
1.9023-2.04920.26111320.21511189X-RAY DIFFRACTION100
2.0492-2.25530.23921310.20911188X-RAY DIFFRACTION100
2.2553-2.58140.24821340.22321198X-RAY DIFFRACTION100
2.5814-3.25120.23621360.22711224X-RAY DIFFRACTION100
3.2512-25.75610.22021370.20121231X-RAY DIFFRACTION95

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