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- PDB-6kqr: A pre-assembled molecular-helical Cascade backbone of Csy3 subuni... -

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Basic information

Entry
Database: PDB / ID: 6kqr
TitleA pre-assembled molecular-helical Cascade backbone of Csy3 subunits from Zymomonas mobilis
ComponentsCRISPR-associated protein Csy3 family
KeywordsRNA BINDING PROTEIN / CRISPR / Cascade / Csy3 / helical backbone
Function / homologyCRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / : / CRISPR-associated protein, Csy3 family
Function and homology information
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsGu, D.H. / Ha, S.C. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1D1A3B03032278 Korea, Republic Of
CitationJournal: Front Microbiol / Year: 2019
Title: A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex.
Authors: Gu, D.H. / Ha, S.C. / Kim, J.S.
History
DepositionAug 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: 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 protein Csy3 family
B: CRISPR-associated protein Csy3 family
C: CRISPR-associated protein Csy3 family
D: CRISPR-associated protein Csy3 family
E: CRISPR-associated protein Csy3 family
F: CRISPR-associated protein Csy3 family
G: CRISPR-associated protein Csy3 family


Theoretical massNumber of molelcules
Total (without water)267,9627
Polymers267,9627
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.181, 116.163, 115.937
Angle α, β, γ (deg.)99.370, 103.120, 103.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CRISPR-associated protein Csy3 family


Mass: 38280.285 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Gene: ZMO2_ZMO0684, ZMO3_ZMO0684 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R4RXD4, UniProt: Q5NPQ2*PLUS

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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: 3.95 Å3/Da / Density % sol: 68.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.899→30 Å / Num. obs: 86087 / % possible obs: 98.4 % / Redundancy: 1.9 % / CC1/2: 0.942 / Net I/σ(I): 16
Reflection shellResolution: 2.899→2.95 Å / Num. unique obs: 4309 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZ9

5uz9


Resolution: 2.899→14.996 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 3417 3.99 %
Rwork0.214 82143 -
obs0.2161 85560 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.61 Å2 / Biso mean: 77.0071 Å2 / Biso min: 34.33 Å2
Refinement stepCycle: final / Resolution: 2.899→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18135 0 0 0 18135
Num. residues----2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118492
X-RAY DIFFRACTIONf_angle_d1.21825040
X-RAY DIFFRACTIONf_chiral_restr0.0622814
X-RAY DIFFRACTIONf_plane_restr0.0073251
X-RAY DIFFRACTIONf_dihedral_angle_d6.65811126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8994-2.94050.4481330.33983221335492
2.9405-2.9840.38661440.3263430357498
2.984-3.03030.37011410.31253378351998
3.0303-3.07960.34321400.28013466360698
3.0796-3.13220.36531450.28253468361398
3.1322-3.18860.37671410.29493367350898
3.1886-3.24930.32981430.28083458360199
3.2493-3.3150.37561460.27233464361098
3.315-3.38620.34061340.26643359349399
3.3862-3.46410.31041400.24353438357899
3.4641-3.54960.30191460.22523483362999
3.5496-3.64420.27961410.21513427356899
3.6442-3.74980.30561470.22273497364499
3.7498-3.86890.27141440.2093416356099
3.8689-4.00460.24021430.19813418356199
4.0046-4.16170.21471450.18523440358599
4.1617-4.34670.24511430.17693492363599
4.3467-4.56970.21161400.16773400354099
4.5697-4.84690.22551470.17753475362299
4.8469-5.20650.22871400.18343417355799
5.2065-5.70410.24321440.20093447359199
5.7041-6.47080.26121460.21643445359199
6.4708-7.94530.2721440.21393421356598
7.9453-14.99580.20461400.18663316345695

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