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

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Basic information

Entry
Database: PDB / ID: 7enh
TitleCrystal structure of cas and anti-cas protein complex
Components
  • AcrIIA14 protein
  • CRISPR-associated endonuclease Cas9
KeywordsVIRAL PROTEIN / Inhibitor / 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 / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease ...: / CRISPR-associated endonuclease Cas9, C-terminal domain / Cas9, PI domain / Cas9, WED domain / CRISPR-Cas9 WED domain / CRISPR-Cas9 PI domain / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
NICKEL (II) ION / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus simulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 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: AcrIIA14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,24913
Polymers31,6032
Non-polymers64611
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.564, 68.564, 118.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-201-

NI

21B-367-

HOH

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Components

#1: Protein CRISPR-associated endonuclease Cas9 / SaCas9


Mass: 19665.371 Da / Num. of mol.: 1 / Fragment: HNH domain
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: Protein AcrIIA14 protein


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)
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium iodide

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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: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.097→50 Å / Num. obs: 29098 / % possible obs: 99.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Χ2: 0.936 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1511.20.71311290.6230.2210.7470.98899.9
2.15-2.211.30.59910960.7680.1840.6270.883100
2.2-2.2611.50.51511420.8430.1560.5390.93499.9
2.26-2.3311.30.44511230.880.1360.4660.931100
2.33-2.411.30.37711320.9260.1150.3940.97100
2.4-2.4910.50.31311340.9450.10.3290.98399.9
2.49-2.5911.70.26511290.9690.0790.2770.998100
2.59-2.7112.40.21911270.980.0630.2281.025100
2.71-2.8512.60.1711660.9880.0490.1771.003100
2.85-3.0312.70.13511330.9930.0380.141.05799.8
3.03-3.2611.80.10411550.9950.0310.1091.094100
3.26-3.5913.80.07911590.9970.0220.0821.024100
3.59-4.1113.60.06511700.9970.0180.0680.91699.9
4.11-5.1812.60.05412050.9980.0150.0560.74199.9
5.18-5012.40.04513020.9990.0130.0470.5799.8

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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: 2.097→48.482 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 2938 10.1 %
Rwork0.1807 26160 -
obs0.1835 29098 91.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.96 Å2 / Biso mean: 32.4186 Å2 / Biso min: 12.57 Å2
Refinement stepCycle: final / Resolution: 2.097→48.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 11 209 2173
Biso mean--44.7 38.84 -
Num. residues----242
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0971-2.13150.3636850.314173755
2.1315-2.16820.2243910.238281760
2.1682-2.20770.25751040.219290666
2.2077-2.25010.24731160.202598475
2.2501-2.2960.23111290.2112113884
2.296-2.3460.23161340.2094123694
2.346-2.40050.25141570.2043136298
2.4005-2.46060.23851460.1983133699
2.4606-2.52710.22751520.21011371100
2.5271-2.60150.24361510.19681331100
2.6015-2.68540.20241530.1931380100
2.6854-2.78140.21361480.18581350100
2.7814-2.89270.19391500.19171364100
2.8927-3.02440.18921510.17861361100
3.0244-3.18380.23651530.17651360100
3.1838-3.38320.19511530.15741322100
3.3832-3.64440.171520.15841385100
3.6444-4.01090.17081550.13671350100
4.0109-4.5910.18341510.14291359100
4.591-5.78260.16641520.17631350100
5.7826-48.4820.25891550.20811361100
Refinement TLS params.Method: refined / Origin x: -24.9807 Å / Origin y: 20.0457 Å / Origin z: -11.4406 Å
111213212223313233
T0.1523 Å20.0155 Å20.039 Å2-0.1865 Å2-0.0172 Å2--0.1472 Å2
L1.465 °20.0957 °2-0.4041 °2-2.1953 °20.3456 °2--1.7129 °2
S0.0657 Å °0.0686 Å °0.1433 Å °-0.0668 Å °0.0835 Å °-0.0728 Å °-0.161 Å °0.0145 Å °-0.1336 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA502 - 645
2X-RAY DIFFRACTION1allB63 - 160
3X-RAY DIFFRACTION1allS1 - 252
4X-RAY DIFFRACTION1allC2 - 14

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