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- PDB-7eni: Crystal structure of cas and anti-cas protein complex -

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Basic information

Entry
Database: PDB / ID: 7eni
TitleCrystal structure of cas and anti-cas protein complex
Components
  • AcrIIA13 protein
  • CRISPR-associated endonuclease Cas9
  • sgRNA (74-MER)
KeywordsVIRAL PROTEIN/RNA / Inhibitor / Complex / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
: / CRISPR-associated endonuclease Cas9, C-terminal domain / Cas9, PI domain / Cas9, WED domain / CRISPR-Cas9 WED domain / CRISPR-Cas9 PI domain / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 ...: / CRISPR-associated endonuclease Cas9, C-terminal domain / Cas9, PI domain / Cas9, WED domain / CRISPR-Cas9 WED domain / CRISPR-Cas9 PI domain / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus schleiferi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.632 Å
AuthorsWang, Y. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91440201 China
CitationJournal: To Be Published
Title: Crystal structure of cas and anti-cas protein complex
Authors: Wang, Y. / Li, X.
History
DepositionApr 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: sgRNA (74-MER)
C: AcrIIA13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,72012
Polymers162,8653
Non-polymers8559
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16440 Å2
ΔGint-168 kcal/mol
Surface area60830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.852, 105.957, 238.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated endonuclease Cas9 / SaCas9


Mass: 124245.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cas9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: J7RUA5, Hydrolases; Acting on ester bonds
#2: RNA chain sgRNA (74-MER)


Mass: 23611.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein AcrIIA13 protein


Mass: 15007.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus schleiferi (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: Tris, Ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.632→50 Å / Num. obs: 65529 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.073 / Rrim(I) all: 0.175 / Χ2: 0.874 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.714.60.91642420.2980.4491.0250.63996.9
2.71-2.784.70.85642210.3920.4120.9540.66196.7
2.78-2.8550.79942510.3290.3710.8850.84596.6
2.85-2.945.20.69842610.550.3170.7690.72897.4
2.94-3.035.20.61743300.7220.2790.6790.73898.3
3.03-3.145.20.50343430.7670.230.5550.87598.4
3.14-3.2750.3943310.8760.1840.4330.99498.7
3.27-3.425.50.28643630.9550.1270.3140.89499.2
3.42-3.65.80.22743720.9720.0990.2480.9999.4
3.6-3.825.70.17344350.9820.0760.1891.03199.4
3.82-4.125.30.13543830.9740.0640.151.0898.8
4.12-4.535.40.10243580.9890.0470.1131.04797.9
4.53-5.195.50.08844220.990.0410.0971.04398.2
5.19-6.535.80.07645030.9940.0340.0830.7799.4
6.53-505.80.04347140.9980.0190.0470.69799

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZZ

5czz


Resolution: 2.632→20.237 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1995 3.43 %
Rwork0.1997 56180 -
obs0.201 58175 87.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.48 Å2 / Biso mean: 41.3131 Å2 / Biso min: 8.81 Å2
Refinement stepCycle: final / Resolution: 2.632→20.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9582 1441 45 352 11420
Biso mean--66.27 33.88 -
Num. residues----1243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.632-2.69720.4389360.3089101922
2.6972-2.770.3491720.2886203145
2.77-2.85130.30271210.2842339174
2.8513-2.9430.28051480.274417991
2.943-3.04790.32471540.2616434696
3.0479-3.16950.27411590.2551447198
3.1695-3.31310.26271620.2364455599
3.3131-3.4870.2831610.2117452699
3.487-3.70420.23381610.1979455099
3.7042-3.98820.24441620.178454599
3.9882-4.38580.19231600.1632452098
4.3858-5.01210.20781620.1539455098
5.0121-6.28310.19261650.1793466499
6.2831-20.2370.19991720.1763483399

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