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

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Basic information

Entry
Database: PDB / ID: 7enr
TitleCrystal structure of cas and anti-cas protein complex
Components
  • AcrIIA14
  • CRISPR-associated endonuclease Cas9
  • sgRNA (98-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
RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.205 Å
AuthorsWang, Y. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31400640 China
CitationJournal: To Be Published
Title: Crystal structure of cas and anti-cas protein complex
Authors: Wang, Y. / Li, X.
History
DepositionApr 19, 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 (98-MER)
C: AcrIIA14


Theoretical massNumber of molelcules
Total (without water)167,4013
Polymers167,4013
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-125 kcal/mol
Surface area65830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.800, 173.800, 185.894
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CRISPR-associated endonuclease Cas9 / SaCas9


Mass: 124158.727 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 (98-MER)


Mass: 31304.432 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 AcrIIA14


Mass: 11937.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus simulans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, EG, Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 15197 / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.056 / Rrim(I) all: 0.117 / Χ2: 0.979 / Net I/σ(I): 5.7 / Num. measured all: 67938
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.2-4.354.60.92215010.6170.4861.0440.949100
4.35-4.524.60.65715310.790.3440.7430.961100
4.52-4.734.50.46115150.8640.2450.5231.024100
4.73-4.984.50.36515260.9040.1940.4141.012100
4.98-5.294.30.28215110.9170.1540.3221.073100
5.29-5.74.30.22315300.9490.1220.2551.039100
5.7-6.274.70.18215140.9640.0950.2060.928100
6.27-7.184.60.12915230.9710.0690.1460.864100
7.18-9.034.20.07915290.9870.0450.0910.768100
9.03-504.40.07215170.9880.0390.0821.17799.8

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Processing

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

5czz


Resolution: 4.205→38.993 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.69 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3068 1446 9.95 %
Rwork0.2603 13093 -
obs0.2649 14539 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.97 Å2 / Biso mean: 42.79 Å2 / Biso min: 0.87 Å2
Refinement stepCycle: final / Resolution: 4.205→38.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8559 1929 0 0 10488
Num. residues----1237
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.2055-4.35560.35261060.286294570
4.3556-4.52980.33031420.2813123089
4.5298-4.73560.31481460.2678135099
4.7356-4.98480.36341510.27571383100
4.9848-5.29640.31121490.27031345100
5.2964-5.70420.33071560.27291378100
5.7042-6.27610.3431510.28841363100
6.2761-7.17930.36991510.28251368100
7.1793-9.02660.24381530.23161369100
9.0266-38.9930.20161410.2002136299

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