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- PDB-5yjc: Structural insights into the CRISPR-Cas-associated ribonuclease a... -

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Basic information

Entry
Database: PDB / ID: 5yjc
TitleStructural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm6
ComponentsCsm6
KeywordsHYDROLASE / CRISPR-Associated proteins / endoribonuclease / higher eukaryotes domain / prokaryotes nucleotide-binding domain
Function / homologyCRISPR-associated protein Csm6 6H domain / CRISPR-associated protein Csm6 / : / Cas_Csm6 CARF domain / : / Cas_Csm6 HEPN domain / Type III-A CRISPR-associated protein Csm6
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.007 Å
AuthorsZhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: To Be Published
Title: Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3 and Csm6
Authors: Zhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Csm6
B: Csm6


Theoretical massNumber of molelcules
Total (without water)67,5242
Polymers67,5242
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-3 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.141, 85.399, 124.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Csm6


Mass: 33761.809 Da / Num. of mol.: 2 / Fragment: UNP residues 147-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (bacteria)
Strain: ATCC 35984 / RP62A / Gene: SERP2456 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HK94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate pH5.0, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→40.4 Å / Num. obs: 44031 / % possible obs: 99 % / Redundancy: 2 % / Net I/σ(I): 31.89

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
SCALAdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.007→40.404 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 2165 4.92 %
Rwork0.1785 --
obs0.1805 44022 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.007→40.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 0 418 4538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094190
X-RAY DIFFRACTIONf_angle_d1.1025642
X-RAY DIFFRACTIONf_dihedral_angle_d9.5842592
X-RAY DIFFRACTIONf_chiral_restr0.065638
X-RAY DIFFRACTIONf_plane_restr0.009716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0074-2.05410.28041270.21382535X-RAY DIFFRACTION91
2.0541-2.10540.32651540.23432758X-RAY DIFFRACTION99
2.1054-2.16240.25041560.19682753X-RAY DIFFRACTION100
2.1624-2.2260.26481510.20582742X-RAY DIFFRACTION99
2.226-2.29780.28811330.22522733X-RAY DIFFRACTION98
2.2978-2.380.24531410.18742776X-RAY DIFFRACTION100
2.38-2.47520.23411280.18882801X-RAY DIFFRACTION100
2.4752-2.58790.25741340.18412788X-RAY DIFFRACTION100
2.5879-2.72430.21431310.20092807X-RAY DIFFRACTION99
2.7243-2.89490.24881550.19922799X-RAY DIFFRACTION100
2.8949-3.11840.21841570.19532805X-RAY DIFFRACTION100
3.1184-3.4320.21811580.18092824X-RAY DIFFRACTION100
3.432-3.92830.19831410.16372846X-RAY DIFFRACTION100
3.9283-4.94780.17591430.14022884X-RAY DIFFRACTION100
4.9478-40.41170.18611560.1643006X-RAY DIFFRACTION99

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