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- PDB-7el1: Structure of a protein from bacteria -

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Basic information

Entry
Database: PDB / ID: 7el1
TitleStructure of a protein from bacteria
Components
  • 100AA
  • CRISPR-associated endonuclease Cas9
  • DNA (28-MER)
  • DNA (5'-D(*TP*TP*GP*AP*AP*TP*AP*G)-3')
  • RNA (73-MER)
KeywordsUNKNOWN FUNCTION
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
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLiu, H. / Zhu, Y. / Huang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31825008 China
National Natural Science Foundation of China (NSFC)31422014 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14.
Authors: Liu, H. / Zhu, Y. / Lu, Z. / Huang, Z.
History
DepositionApr 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 endonuclease Cas9
B: RNA (73-MER)
C: DNA (28-MER)
D: DNA (5'-D(*TP*TP*GP*AP*AP*TP*AP*G)-3')
E: 100AA


Theoretical massNumber of molelcules
Total (without water)170,4825
Polymers170,4825
Non-polymers00
Water2,270126
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)330.585, 105.222, 68.551
Angle α, β, γ (deg.)90, 92.71, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AE

#1: Protein CRISPR-associated endonuclease Cas9 / SaCas9


Mass: 124083.648 Da / Num. of mol.: 1 / Mutation: N580A, C946A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cas9 / Production host: Escherichia coli (E. coli)
References: UniProt: J7RUA5, Hydrolases; Acting on ester bonds
#5: Protein 100AA


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

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (28-MER)


Mass: 8469.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#4: DNA chain DNA (5'-D(*TP*TP*GP*AP*AP*TP*AP*G)-3')


Mass: 2465.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)

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RNA chain / Non-polymers , 2 types, 127 molecules B

#2: RNA chain RNA (73-MER)


Mass: 23525.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0M sodium citrate dihydrate, 0.3M imidazol-Hcl (pH 10.0), 0.02M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.22→68.47 Å / Num. obs: 116344 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 2.22→2.34 Å / Rmerge(I) obs: 0.714 / Num. unique obs: 16935

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Processing

Software
NameVersionClassification
PHENIXv1.11refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5czz

5czz


Resolution: 2.22→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2423 5623 -
Rwork0.2132 --
obs-116174 99.9 %
Refinement stepCycle: LAST / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 2270 0 126 11628
LS refinement shellResolution: 2.22→2.34 Å /
Num. reflection% reflection
obs16935 100 %

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