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- PDB-9xy8: One of a series of engineered variants of I-OnuI meganuclease tar... -

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Basic information

Entry
Database: PDB / ID: 9xy8
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
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: 2.49 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

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Assembly

Deposited unit
A: eI-OnuI_P456_CCC
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6857
Polymers50,4213
Non-polymers2644
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-86 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.222, 76.159, 167.753
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


Mass: 34447.770 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: 7895.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8078.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 94 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES pH 7.0, 200mM ammonium sulfate, 30% PEG 3350

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.54209 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54209 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 18355 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.07 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Χ2: 0.731 / Net I/σ(I): 7 / Num. measured all: 113959
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.586.10.29733140.9570.1290.3250.5197.1
2.58-2.686.40.23333490.9730.0990.2530.52399.5
2.68-2.86.20.18234790.980.0780.1990.52999.7
2.8-2.956.10.14433620.9880.0630.1580.553100
2.95-3.146.50.11133560.9930.0470.120.60599.9
3.14-3.386.20.07533800.9960.0340.0830.72699.9
3.38-3.726.20.06533870.9960.0290.0710.88299.6
3.72-4.266.40.05634200.9970.0240.0610.84799.7
4.26-5.366.30.05333860.9970.0230.0580.902100
5.36-505.80.06134170.9940.0280.0681.19699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.47 Å45.07 Å
Translation6.47 Å45.07 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→45.073 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1831 10.01 %
Rwork0.193 16468 -
obs0.1988 18299 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.86 Å2 / Biso mean: 40.1273 Å2 / Biso min: 18.4 Å2
Refinement stepCycle: final / Resolution: 2.49→45.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 1063 30 90 3532
Biso mean--59.67 36.4 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043593
X-RAY DIFFRACTIONf_angle_d0.5945068
X-RAY DIFFRACTIONf_chiral_restr0.039572
X-RAY DIFFRACTIONf_plane_restr0.003459
X-RAY DIFFRACTIONf_dihedral_angle_d19.6391952
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4903-2.55760.33011330.2417119797
2.5576-2.63290.29261400.2281126099
2.6329-2.71790.32331360.21761220100
2.7179-2.8150.33981400.23461270100
2.815-2.92770.31881370.24291227100
2.9277-3.06090.29561420.22961270100
3.0609-3.22220.30081380.22191246100
3.2222-3.4240.28081400.2011260100
3.424-3.68830.25841400.20131254100
3.6883-4.05930.24671410.18531271100
4.0593-4.64610.19041430.16231282100
4.6461-5.85160.20141460.16771317100
5.8516-45.070.20611550.16921394100

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