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- PDB-6vjg: Csx3-I222 Crystal Form at 1.8 Angstrom Resolution -

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Basic information

Entry
Database: PDB / ID: 6vjg
TitleCsx3-I222 Crystal Form at 1.8 Angstrom Resolution
ComponentsCRISPR-associated protein, Csx3 family
KeywordsRNA BINDING PROTEIN / CRISPR / Cas / CARF / RNase
Function / homologyCRISPR-associated protein Csx3 / CRISPR-associated protein (Cas_csx3) / CRISPR-associated protein, Csx3 family / Uncharacterized protein AF_1864
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 8774 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrown, S. / Charbonneau, A. / Burman, N. / Gauvin, C.C. / Lawrence, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103474 United States
National Science Foundation (NSF, United States)MCB-1413534 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Csx3 is a cyclic oligonucleotide phosphodiesterase associated with type III CRISPR-Cas that degrades the second messenger cA 4 .
Authors: Brown, S. / Gauvin, C.C. / Charbonneau, A.A. / Burman, N. / Lawrence, C.M.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: CRISPR-associated protein, Csx3 family


Theoretical massNumber of molelcules
Total (without water)12,6951
Polymers12,6951
Non-polymers00
Water97354
1
A: CRISPR-associated protein, Csx3 family

A: CRISPR-associated protein, Csx3 family


Theoretical massNumber of molelcules
Total (without water)25,3902
Polymers25,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area2200 Å2
ΔGint-20 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.450, 61.540, 70.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-232-

HOH

21A-238-

HOH

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Components

#1: Protein CRISPR-associated protein, Csx3 family


Mass: 12694.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 8774 (archaea)
Gene: AFULGI_00021190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A075WFT8, UniProt: O28415*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.43 Å3/Da / Density % sol: 45.94 %
Description: Rhombus shaped plates approximately 115 x 125 um.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 45% 2-methyl-2,4-pentanediol, 0.1 M Tris pH 8.5, 0.2 M Ammonium Phosphate Monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→46.29 Å / Num. obs: 10996 / % possible obs: 98.9 % / Redundancy: 4.8 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.032 / Rrim(I) all: 0.071 / Χ2: 0.933 / Net I/σ(I): 27.305
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 510 / CC1/2: 0.917 / CC star: 0.978 / Χ2: 0.53 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZG

3wzg


Resolution: 1.8→46.25 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.0208
RfactorNum. reflection% reflection
Rfree0.216 1096 9.97 %
Rwork0.1873 --
obs0.1902 10996 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 0 54 891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063858
X-RAY DIFFRACTIONf_angle_d0.81421162
X-RAY DIFFRACTIONf_chiral_restr0.0607133
X-RAY DIFFRACTIONf_plane_restr0.007146
X-RAY DIFFRACTIONf_dihedral_angle_d14.7731513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.25071330.2371201X-RAY DIFFRACTION99.55
1.88-1.980.23181370.20661227X-RAY DIFFRACTION99.63
1.98-2.110.21521310.18841215X-RAY DIFFRACTION99.48
2.11-2.270.27811370.19171231X-RAY DIFFRACTION99.56
2.27-2.50.22841350.19181222X-RAY DIFFRACTION99.63
2.5-2.860.2551380.19681238X-RAY DIFFRACTION99.71
2.86-3.60.19861390.1791256X-RAY DIFFRACTION99.71
3.6-46.250.19391460.18131310X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: 3.95343482676 Å / Origin y: 14.817631476 Å / Origin z: 9.75784545109 Å
111213212223313233
T0.225469696334 Å2-0.0145599630819 Å2-0.0157126921169 Å2-0.305953761259 Å2-0.0306152648936 Å2--0.188178838298 Å2
L3.22234602538 °20.710180578083 °20.512391262883 °2-2.92455551705 °2-0.533880885072 °2--5.74947382986 °2
S0.0130425019169 Å °-0.515381285527 Å °0.192292526812 Å °0.255691489078 Å °-0.192632633819 Å °-0.14110519196 Å °-0.301862783829 Å °0.420776442144 Å °0.13194911703 Å °
Refinement TLS groupSelection details: all

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