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- PDB-5yi6: CRISPR associated protein Cas6 -

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Basic information

Entry
Database: PDB / ID: 5yi6
TitleCRISPR associated protein Cas6
ComponentsCRISPR-associated endoribonuclease Cas6 1
KeywordsHYDROLASE
Function / homology
Function and homology information


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
PHOSPHATE ION / CRISPR-associated endoribonuclease Cas6 1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.852 Å
AuthorsKo, T.P. / Hsieh, T.J. / Chen, Y.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology, R.O.C.MOST105-0210-01-12-01 Taiwan
Ministry of Science and Technology, ROCMOST106-0210-01-15-04 Taiwan
National Science Council (Taiwan)NSC99-2313-B-241-001 Taiwan
National Science Council (Taiwan)NSC100-2313-B-241-006 Taiwan
CitationJournal: Crystals / Year: 2018
Title: Expression, Purification, Crystallization, and X-ray Structural Analysis of CRISPR-Associated Protein Cas6 from Methanocaldococcus jannaschii
Authors: Lee, M.C. / Tseng, S.T. / Yang, J.C. / Hsieh, T.J. / Wu, S.C. / Kuan, S.M. / Chen, M.J. / Chang, M.C. / Wang, C.C. / Chen, H.L. / Fang, G.C. / Huang, W.J. / Ko, T.P. / Chen, Y.
History
DepositionOct 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas6 1
B: CRISPR-associated endoribonuclease Cas6 1
C: CRISPR-associated endoribonuclease Cas6 1
D: CRISPR-associated endoribonuclease Cas6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,05134
Polymers125,2134
Non-polymers2,83830
Water19,7801098
1
A: CRISPR-associated endoribonuclease Cas6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0609
Polymers31,3031
Non-polymers7578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR-associated endoribonuclease Cas6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9658
Polymers31,3031
Non-polymers6627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CRISPR-associated endoribonuclease Cas6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0609
Polymers31,3031
Non-polymers7578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CRISPR-associated endoribonuclease Cas6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9658
Polymers31,3031
Non-polymers6627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.835, 85.255, 100.065
Angle α, β, γ (deg.)90.00, 118.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CRISPR-associated endoribonuclease Cas6 1


Mass: 31303.361 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: cas6a / Production host: Escherichia coli (E. coli)
References: UniProt: Q57820, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES sodium salt pH7.5, 600mM NaH2PO4, 600mM KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.852→29.087 Å / Num. obs: 125357 / % possible obs: 99.7 % / Redundancy: 3.7 % / Net I/σ(I): 17.28
Reflection shellResolution: 1.8524→1.9186 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.039 / Num. unique obs: 12437 / CC1/2: 0.809 / Rpim(I) all: 0.586 / Rrim(I) all: 0.301 / Rsym value: 0.431 / Χ2: 0.59 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I4H

3i4h


Resolution: 1.852→29.087 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.83
RfactorNum. reflection% reflection
Rfree0.1945 2010 1.6 %
Rwork0.1668 --
obs0.1673 125321 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.852→29.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8038 0 154 1098 9290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118350
X-RAY DIFFRACTIONf_angle_d1.02511217
X-RAY DIFFRACTIONf_dihedral_angle_d10.2614983
X-RAY DIFFRACTIONf_chiral_restr0.071149
X-RAY DIFFRACTIONf_plane_restr0.0071406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8524-1.89870.27491358383X-RAY DIFFRACTION96
1.8987-1.95010.25291458841X-RAY DIFFRACTION100
1.9501-2.00740.221458771X-RAY DIFFRACTION100
2.0074-2.07220.20871408803X-RAY DIFFRACTION100
2.0722-2.14630.20781478794X-RAY DIFFRACTION100
2.1463-2.23220.21091448836X-RAY DIFFRACTION100
2.2322-2.33370.22511410.17438796X-RAY DIFFRACTION100
2.3337-2.45670.23431518806X-RAY DIFFRACTION100
2.4567-2.61050.22211468849X-RAY DIFFRACTION100
2.6105-2.81190.23231408831X-RAY DIFFRACTION100
2.8119-3.09460.20391448872X-RAY DIFFRACTION100
3.0946-3.54170.18121410.15918864X-RAY DIFFRACTION100
3.5417-4.45960.1641440.13888869X-RAY DIFFRACTION99
4.4596-29.080.16071470.15948996X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 101.3435 Å / Origin y: 58.2168 Å / Origin z: 29.3865 Å
111213212223313233
T0.1302 Å2-0.0002 Å20.0132 Å2-0.1119 Å20.0038 Å2--0.1153 Å2
L0.6941 °20.05 °20.3528 °2-0.0252 °20.0187 °2--0.197 °2
S0.0192 Å °-0.0101 Å °-0.0092 Å °0.0123 Å °-0.0055 Å °-0.0102 Å °0.0044 Å °-0.0074 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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