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- PDB-9b72: Rec2 Domain from G. stearothermophilus Cas9 -

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Basic information

Entry
Database: PDB / ID: 9b72
TitleRec2 Domain from G. stearothermophilus Cas9
ComponentsCRISPR-associated endonuclease Cas9
KeywordsRNA BINDING PROTEIN / CRISPR Cas9 / nucleic acid binding protein
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Cas9, alpha-helical lobe domain / Cas9 alpha-helical lobe domain / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsD'Ordine, A.M. / Belato, H.B. / Lisi, G.P. / Jogl, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2025
Title: Structural and dynamic impacts of single-atom disruptions to guide RNA interactions within the recognition lobe of Geobacillus stearothermophilus Cas9.
Authors: Belato, H.B. / Knight, A.L. / D'Ordine, A.M. / Pindi, C. / Fan, Z. / Luo, J. / Palermo, G. / Jogl, G. / Lisi, G.P.
History
DepositionMar 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)25,4001
Polymers25,4001
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.938, 72.353, 50.807
Angle α, β, γ (deg.)90.000, 122.719, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 25399.807 Da / Num. of mol.: 1 / Fragment: residues 240-456 (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: cas9, B4109_0323 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A150MP45, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.15 M calcium chloride, 15 % polyethylene glycol 6000, 0.1 M HEPES at pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.49→42.75 Å / Num. obs: 43163 / % possible obs: 98.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.98 Å2 / CC1/2: 0.986 / Net I/σ(I): 11.2
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 2065 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→42.75 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1966 2221 5.15 %
Rwork0.1705 40931 -
obs0.1718 43152 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.96 Å2
Refinement stepCycle: LAST / Resolution: 1.49→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 0 195 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541645
X-RAY DIFFRACTIONf_angle_d0.76082215
X-RAY DIFFRACTIONf_chiral_restr0.0712232
X-RAY DIFFRACTIONf_plane_restr0.0084286
X-RAY DIFFRACTIONf_dihedral_angle_d4.8853218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.40871430.34632493X-RAY DIFFRACTION97.34
1.52-1.560.40991240.29462522X-RAY DIFFRACTION97.75
1.56-1.60.2881390.23162522X-RAY DIFFRACTION97.9
1.6-1.640.2681290.1932558X-RAY DIFFRACTION97.89
1.64-1.690.22381460.16952504X-RAY DIFFRACTION98.08
1.69-1.740.19671290.16832538X-RAY DIFFRACTION98.27
1.74-1.810.2161420.17532549X-RAY DIFFRACTION98.5
1.81-1.880.21871410.19952560X-RAY DIFFRACTION98.5
1.88-1.960.22091390.17662555X-RAY DIFFRACTION98.83
1.96-2.070.2111720.16142515X-RAY DIFFRACTION98.97
2.07-2.20.21821500.16062580X-RAY DIFFRACTION99.24
2.2-2.370.18971250.15412564X-RAY DIFFRACTION99.26
2.37-2.60.18251430.16092590X-RAY DIFFRACTION99.49
2.6-2.980.18821350.16962594X-RAY DIFFRACTION99.6
2.98-3.750.20461330.17032616X-RAY DIFFRACTION99.82
3.75-42.750.16311310.16372671X-RAY DIFFRACTION99.96

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