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- PDB-3i4h: Crystal structure of Cas6 in Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 3i4h
TitleCrystal structure of Cas6 in Pyrococcus furiosus
Componentsendoribonuclease
KeywordsHYDROLASE / endoribonuclease
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
: / CRISPR associated protein Cas6, C-terminal / CRISPR-associated protein Cas6, N-terminal / Alpha-Beta Plaits - #1890 / CRISPR-associated protein Cas6, N-terminal domain superfamily / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas6
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsCarte, J. / Wang, R. / Li, H. / Terns, R.M. / Terns, M.P.
CitationJournal: Genes Dev. / Year: 2008
Title: Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes
Authors: Carte, J. / Wang, R. / Li, H. / Terns, R.M. / Terns, M.P.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: endoribonuclease


Theoretical massNumber of molelcules
Total (without water)31,7941
Polymers31,7941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.745, 84.745, 81.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein endoribonuclease


Mass: 31793.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S4

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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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02 M Magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.0, 15% v/v 2-Propanol, temperature 303K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 1.5418,1.5621,1.7321
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: mirror
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.56211
31.73211
ReflectionResolution: 1.8→20.5 Å / Num. all: 29842 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 17.7 % / Rsym value: 0.059 / Net I/σ(I): 2.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 17.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.059 / % possible all: 48

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.25→20.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.294 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28896 832 5.2 %RANDOM
Rwork0.22635 ---
obs0.22951 15277 100 %-
all-1089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 0 0 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221971
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4291.9692660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0615229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46223.22693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7191510
X-RAY DIFFRACTIONr_chiral_restr0.1950.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021505
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.2790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.21288
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1251.51217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3321870
X-RAY DIFFRACTIONr_scbond_it4.1423907
X-RAY DIFFRACTIONr_scangle_it5.734.5790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 53 -
Rwork0.281 936 -
obs--100 %

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