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- PDB-9xy9: One of a series of engineered variants of I-OnuI meganuclease tar... -

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Basic information

Entry
Database: PDB / ID: 9xy9
TitleOne of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence
Components
  • (DNA (26-MER)) x 2
  • eI-OnuI_P456_ACA
KeywordsDNA BINDING PROTEIN / meganuclease / structure prediction / protein engineering / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.995 Å
AuthorsWerther, R. / Stoddard, B.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM139752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM105691 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM148166 United States
CitationJournal: To Be Published
Title: Prediction, modeling and design of protein-DNA recognition via computational and machine learning approaches: accomplishments and remaining challenges
Authors: Esler, M.A. / Werther, R. / Bradley, P. / Stoddard, B.L.
History
DepositionAug 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eI-OnuI_P456_ACA
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,03412
Polymers50,5803
Non-polymers4549
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-88 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.351, 76.613, 167.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein eI-OnuI_P456_ACA


Mass: 34608.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (26-MER)


Mass: 7943.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8028.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 118 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 27.5% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.995→50 Å / Num. obs: 35138 / % possible obs: 99.1 % / Redundancy: 12.9 % / Biso Wilson estimate: 38.96 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 0.936 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0712.60.71934590.9040.2090.750.78898.4
2.07-2.1512.80.49933990.9510.1440.520.81598.6
2.15-2.2513.40.3534330.9740.0980.3640.86698.8
2.25-2.3713.40.25934380.9850.0730.2690.90698.9
2.37-2.5212.70.18734650.9920.0540.1950.97299
2.52-2.7112.80.13134880.9950.0380.1361.08799.1
2.71-2.9913.40.09235300.9980.0260.0950.98699.4
2.99-3.4212.80.06335270.9980.0190.0660.98499.5
3.42-4.3113.10.05236030.9990.0150.0541.01199.6
4.31-5012.10.04537960.9990.0130.0470.93599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.67 Å45.12 Å
Translation5.67 Å45.12 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→45.12 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2618 1998 5.7 %
Rwork0.2132 33085 -
obs0.2159 35083 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.75 Å2 / Biso mean: 42.8689 Å2 / Biso min: 21.9 Å2
Refinement stepCycle: final / Resolution: 1.995→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 1060 54 109 3550
Biso mean--51.19 39.7 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153576
X-RAY DIFFRACTIONf_angle_d1.3825049
X-RAY DIFFRACTIONf_chiral_restr0.079569
X-RAY DIFFRACTIONf_plane_restr0.009461
X-RAY DIFFRACTIONf_dihedral_angle_d20.8141925
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.995-2.04460.29221330.2543220594
2.0446-2.09990.33411400.2499231599
2.0999-2.16160.31331390.2351230899
2.1616-2.23140.33031410.2253231899
2.2314-2.31120.27091410.2325234499
2.3112-2.40370.30091410.2325233399
2.4037-2.51310.2811410.2375233399
2.5131-2.64560.30471430.239236699
2.6456-2.81130.29191440.238238399
2.8113-3.02830.28151440.23622370100
3.0283-3.3330.25141440.21732377100
3.333-3.81510.26091440.20742396100
3.8151-4.80570.23371480.18252457100
4.8057-45.120.23281550.20162580100

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