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- PDB-7ei1: Structure of Pyrococcus furiosus Cas1Cas2 complex -

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Basic information

Entry
Database: PDB / ID: 7ei1
TitleStructure of Pyrococcus furiosus Cas1Cas2 complex
Components
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2
KeywordsIMMUNE SYSTEM / CRISPR / adaptation
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, HMARI/TNEAP subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 ...CRISPR-associated protein Cas1, HMARI/TNEAP subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas1 / CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsYu, Y. / Chen, Q.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: A distinct structure of Cas1-Cas2 complex provides insights into the mechanism for the longer spacer acquisition in Pyrococcus furiosus.
Authors: Tang, D. / Li, H. / Wu, C. / Jia, T. / He, H. / Yao, S. / Yu, Y. / Chen, Q.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endonuclease Cas1
G: CRISPR-associated endonuclease Cas1
H: CRISPR-associated endonuclease Cas1
Q: CRISPR-associated endoribonuclease Cas2
R: CRISPR-associated endoribonuclease Cas2
S: CRISPR-associated endoribonuclease Cas2
T: CRISPR-associated endoribonuclease Cas2
U: CRISPR-associated endoribonuclease Cas2
V: CRISPR-associated endoribonuclease Cas2
W: CRISPR-associated endoribonuclease Cas2
X: CRISPR-associated endoribonuclease Cas2
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endonuclease Cas1
N: CRISPR-associated endonuclease Cas1
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
O: CRISPR-associated endonuclease Cas1
P: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)680,57224
Polymers680,57224
Non-polymers00
Water00
1
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
Q: CRISPR-associated endoribonuclease Cas2
R: CRISPR-associated endoribonuclease Cas2
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)170,1436
Polymers170,1436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endoribonuclease Cas2
T: CRISPR-associated endoribonuclease Cas2
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)170,1436
Polymers170,1436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2
V: CRISPR-associated endoribonuclease Cas2
M: CRISPR-associated endonuclease Cas1
N: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)170,1436
Polymers170,1436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: CRISPR-associated endonuclease Cas1
H: CRISPR-associated endonuclease Cas1
W: CRISPR-associated endoribonuclease Cas2
X: CRISPR-associated endoribonuclease Cas2
O: CRISPR-associated endonuclease Cas1
P: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)170,1436
Polymers170,1436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.763, 180.473, 338.847
Angle α, β, γ (deg.)90.000, 94.428, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 37539.426 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: cas1, PFC_04810 / Production host: Escherichia coli (E. coli)
References: UniProt: I6TWX9, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endoribonuclease Cas2


Mass: 9992.677 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: cas2, PFC_04805 / Production host: Escherichia coli (E. coli)
References: UniProt: I6V1H0, Hydrolases; Acting on ester bonds

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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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% w/v polyethylene glycol 6000, 6% v/v ethylene glycol, 0.1M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 107906 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.49 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.063 / Net I/σ(I): 11.3
Reflection shellResolution: 3.9→3.97 Å / Num. unique obs: 5377 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WJ0,4TN0

4wj0

4tn0


Resolution: 3.9→36.53 Å / SU ML: 0.6278 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.4845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3281 969 0.96 %
Rwork0.2805 99821 -
obs0.281 100790 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.49 Å2
Refinement stepCycle: LAST / Resolution: 3.9→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46274 0 0 0 46274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003547206
X-RAY DIFFRACTIONf_angle_d0.765263536
X-RAY DIFFRACTIONf_chiral_restr0.04736975
X-RAY DIFFRACTIONf_plane_restr0.00428001
X-RAY DIFFRACTIONf_dihedral_angle_d5.741828534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.110.4571970.320410030X-RAY DIFFRACTION65.73
4.11-4.360.30621230.293214375X-RAY DIFFRACTION94.86
4.36-4.70.31781610.269315161X-RAY DIFFRACTION99.58
4.7-5.170.31941460.268915150X-RAY DIFFRACTION99.49
5.17-5.920.34111480.289915105X-RAY DIFFRACTION99.21
5.92-7.440.33461560.304415197X-RAY DIFFRACTION99.38
7.44-36.530.2831380.248314803X-RAY DIFFRACTION95.59

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