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- PDB-9n3a: N-Terminal Domain of CRISPR-associated DinG -

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Basic information

Entry
Database: PDB / ID: 9n3a
TitleN-Terminal Domain of CRISPR-associated DinG
ComponentsCRISPR-associated DinG
KeywordsPROTEIN BINDING / type IV CRISPR / DinG / Csf Complex / NTD
Function / homologyATP-dependent helicase, C-terminal / Helicase C-terminal domain / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / helicase activity / nucleic acid binding / P-loop containing nucleoside triphosphate hydrolase / ATP binding / CasDinG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRedman, O. / Jackson, R.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138080 United States
CitationJournal: To Be Published
Title: Locked and loaded: mechanisms of CasDinG recruitment to the type IV-A1 CRISPR effector complex
Authors: Kiernan, K.A. / Williams, A.A. / Redman, O. / Jenkins, E. / Taylor, D.W. / Jackson, R.N.
History
DepositionJan 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated DinG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8805
Polymers10,4961
Non-polymers3844
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.669, 39.304, 83.097
Angle α, β, γ (deg.)90.000, 95.045, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein CRISPR-associated DinG / CasDinG


Mass: 10495.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: A0AA82WPF0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.146137 Å3/Da / Density % sol: 42.72334 % / Description: tabular
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Mother liquor consisted of 18% PEG 3350, 0.1M Na citrate buffer (pH 4.0), and 0.2M Ammonium Sulfate. Mother liquor was mixed with concentrated protein (12 mg/ml) at a ratio of 2:1.5 (protein solution : ML)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å / Voltage: 40 kV
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→26.87 Å / Num. obs: 18483 / % possible obs: 73.27 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.041 / Rrim(I) all: 0.073 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.21-35.513.080.03745.821230.9960.0260.04599.57
3.34-4.213.060.04443.320010.9960.030.053100
2.92-3.343.120.05237.66600.9920.0350.063100
2.65-2.923.10.05531.96520.9940.0370.067100
2.46-2.653.110.06228.26480.9890.0420.076100
2.32-2.463.070.06725.36470.9920.0450.081100
2.2-2.323.070.0724.16560.9890.0470.085100
2.11-2.23.050.0820.76550.9860.0550.098100
2.02-2.113.10.091176470.9840.0620.111100
1.95-2.023.070.104156250.9810.0710.126100
1.89-1.953.070.11812.26590.970.0810.144100
1.84-1.893.070.14110.36360.9580.0950.171100
1.79-1.842.680.1557.16410.9550.1090.1998.62
1.75-1.792.370.1725.75240.8930.1310.21779.76
1.71-1.752.220.1565.14040.930.1270.20263.12
1.67-1.712.070.1644.33380.9340.1340.21352.32
1.64-1.671.860.1743.22360.9380.1520.23237.82
1.61-1.641.70.1872.91960.9270.1720.25430.72
1.58-1.611.470.2222.41070.8850.2150.3116.14
1.55-1.581.090.231.3340.9210.230.3265.45

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
Coot0.9.8.96model building
PHASER2.8.3phasing
Aimless0.7.15data scaling
pointless1.12.16data scaling
DIALS2021.11.1data reduction
HKL-3000720data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→26.87 Å / SU ML: 0.1111 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.0808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1617 904 4.89 %
Rwork0.1319 17577 -
obs0.1334 18481 73.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 20 126 849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082752
X-RAY DIFFRACTIONf_angle_d0.95991033
X-RAY DIFFRACTIONf_chiral_restr0.0508125
X-RAY DIFFRACTIONf_plane_restr0.0108131
X-RAY DIFFRACTIONf_dihedral_angle_d13.6247275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.650.1603360.1976487X-RAY DIFFRACTION12.5
1.65-1.780.1925830.17491671X-RAY DIFFRACTION41.75
1.78-1.950.21261840.14563674X-RAY DIFFRACTION91.1
1.96-2.240.17261720.13243928X-RAY DIFFRACTION98.2
2.24-2.820.16032050.12313929X-RAY DIFFRACTION98.03
2.82-26.870.14172240.12593888X-RAY DIFFRACTION97.72

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