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- PDB-9q7z: One of a series of engineered variants of I-OnuI meganuclease tar... -

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Basic information

Entry
Database: PDB / ID: 9q7z
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_CGG
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: 3.319 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_CGG
B: DNA (26-MER)
C: DNA (26-MER)
D: eI-OnuI_P456_CGG
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8048
Polymers100,7246
Non-polymers802
Water1629
1
A: eI-OnuI_P456_CGG
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4425
Polymers50,3623
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-77 kcal/mol
Surface area18850 Å2
MethodPISA
2
D: eI-OnuI_P456_CGG
E: DNA (26-MER)
F: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)50,3623
Polymers50,3623
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-54 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)327.795, 40.472, 78.235
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein eI-OnuI_P456_CGG


Mass: 34388.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (26-MER)


Mass: 7975.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7998.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 150MM DL-Malic acid pH 7.0, 25% 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: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 15108 / % possible obs: 97 % / Redundancy: 5.3 % / Biso Wilson estimate: 94.12 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.1 / Χ2: 1.026 / Net I/σ(I): 12.2 / Num. measured all: 79880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.423.40.15412270.9940.0870.1780.94279.8
3.42-3.5540.18614250.9930.0990.2120.83594.5
3.55-3.724.60.19715390.9890.1010.2220.8597.8
3.72-3.9150.18615030.9830.0920.2090.96899.5
3.91-4.165.40.13115460.9910.0620.1461.07699.7
4.16-4.486.10.11915510.9940.0530.131.05599.6
4.48-4.9360.09715290.9940.0440.1071.07999.7
4.93-5.645.80.09115670.9920.0420.1011.06499.9
5.64-7.16.30.08315660.9940.0360.091.09199.8
7.1-505.60.07316550.9950.0330.0811.10499.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.85 Å40.87 Å
Translation5.85 Å40.87 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.319→40.874 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1503 10.01 %
Rwork0.2394 --
obs0.244 15020 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.319→40.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 2120 2 9 6030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036338
X-RAY DIFFRACTIONf_angle_d0.5339090
X-RAY DIFFRACTIONf_dihedral_angle_d17.8293282
X-RAY DIFFRACTIONf_chiral_restr0.0351055
X-RAY DIFFRACTIONf_plane_restr0.002822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.319-3.42590.3875900.2942842X-RAY DIFFRACTION66
3.4259-3.54830.4221400.29261138X-RAY DIFFRACTION91
3.5483-3.69030.36371230.28611234X-RAY DIFFRACTION96
3.6903-3.85810.38351320.29061243X-RAY DIFFRACTION99
3.8581-4.06130.32521570.2761276X-RAY DIFFRACTION99
4.0613-4.31550.3311270.25651250X-RAY DIFFRACTION99
4.3155-4.64830.26981460.23821295X-RAY DIFFRACTION100
4.6483-5.11530.27281450.22711286X-RAY DIFFRACTION100
5.1153-5.85360.32781470.24431286X-RAY DIFFRACTION100
5.8536-7.36790.27121410.25661300X-RAY DIFFRACTION100
7.3679-40.870.21171550.19171367X-RAY DIFFRACTION99

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