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- PDB-9xy6: One of a series of engineered variants of I-OnuI meganuclease tar... -

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Basic information

Entry
Database: PDB / ID: 9xy6
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_CCC_2
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.693 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_CCC_2
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5937
Polymers50,4113
Non-polymers1824
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-95 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.185, 64.283, 167.825
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_CCC_2


Mass: 34438.766 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: 7910.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8062.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 25 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.25M DL-Malic acid pH 7.0, 35% PEG 3350, 100mM Tris pH 7.0

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.693→50 Å / Num. obs: 12932 / % possible obs: 95 % / Redundancy: 12.5 % / Biso Wilson estimate: 49.11 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Χ2: 1.013 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.89.40.3879680.9630.1280.410.94573.8
2.8-2.9110.70.29911030.9870.0910.3130.95682.4
2.91-3.0411.70.27812380.990.0820.2910.99794.2
3.04-3.212.60.20613180.9970.0590.2151.02599.2
3.2-3.413.20.091135410.0260.0951.02499.7
3.4-3.6613.60.08813430.9990.0250.0921.02399.7
3.66-4.0313.60.07213650.9990.020.0751.015100
4.03-4.6213.50.05313600.9990.0150.0551.0399.9
4.62-5.8113.30.048138910.0140.051.076100
5.81-5012.40.03914940.9990.0120.0410.97899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.69 Å38.4 Å
Translation2.69 Å38.4 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.693→38.398 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2935 1268 10.02 %
Rwork0.239 11388 -
obs0.2445 12656 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.92 Å2 / Biso mean: 46.0275 Å2 / Biso min: 34.77 Å2
Refinement stepCycle: final / Resolution: 2.693→38.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 1058 13 21 3302
Biso mean--51.93 41.17 -
Num. residues----341
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6931-2.80090.44041070.37596573
2.8009-2.92840.46641240.3536111284
2.9284-3.08270.39641420.341128995
3.0827-3.27570.33331430.2961126998
3.2757-3.52850.35431470.258131397
3.5285-3.88330.30751460.2385133198
3.8833-4.44450.24131460.2122130497
4.4445-5.59680.2551490.2043135497
5.5968-38.3980.22931640.1873145199

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