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- PDB-9xy5: One of a series of engineered variants of I-OnuI meganuclease tar... -

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Basic information

Entry
Database: PDB / ID: 9xy5
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_AGT_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: 2.612 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_AGT_2
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6336
Polymers50,4913
Non-polymers1423
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-85 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.171, 68.382, 165.541
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_AGT_2


Mass: 34519.793 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: 7974.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7997.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 38 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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.: 35 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 8000, 100mM HEPES 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: Oct 31, 1017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.612→50 Å / Num. obs: 13760 / % possible obs: 97 % / Redundancy: 5.1 % / Biso Wilson estimate: 44.68 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.1 / Χ2: 0.999 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.715.20.66313140.7920.3070.7340.93497.6
2.71-2.825.10.52913770.90.2460.5860.93897
2.82-2.955.10.4113290.9110.1910.4550.95897.6
2.95-3.1150.28213460.9590.1320.3130.97996.1
3.11-3.34.90.1313460.9980.0620.1451.02195.9
3.3-3.564.80.08213440.9970.0390.0920.99395.8
3.56-3.914.70.08313370.9950.040.0931.04294.2
3.91-4.484.60.05913560.9970.0290.0671.01395.8
4.48-5.6450.05314630.9980.0260.0590.99499.9
5.64-506.10.03915480.9990.0170.0431.08799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.51 Å42.94 Å
Translation5.51 Å42.94 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.612→42.943 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1371 10.01 %
Rwork0.2104 12325 -
obs0.2162 13696 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.02 Å2 / Biso mean: 41.0797 Å2 / Biso min: 19.68 Å2
Refinement stepCycle: final / Resolution: 2.612→42.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 1060 12 35 3342
Biso mean--61.61 30.43 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053479
X-RAY DIFFRACTIONf_angle_d0.7314934
X-RAY DIFFRACTIONf_chiral_restr0.042564
X-RAY DIFFRACTIONf_plane_restr0.004447
X-RAY DIFFRACTIONf_dihedral_angle_d21.2111858
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6123-2.70570.39141300.3221117597
2.7057-2.8140.37651380.2926123597
2.814-2.94210.33931330.2778119498
2.9421-3.09710.32631340.2653121296
3.0971-3.29110.32691350.2474119995
3.2911-3.54510.26291330.198120696
3.5451-3.90160.25711330.1945120194
3.9016-4.46570.24181360.1705121696
4.4657-5.62430.2451450.17571313100
5.6243-42.940.20411540.1934137499
Refinement TLS params.Method: refined / Origin x: 48.6961 Å / Origin y: 2.1859 Å / Origin z: 34.9243 Å
111213212223313233
T0.2122 Å20.0069 Å20.0071 Å2-0.2146 Å2-0.0155 Å2--0.3185 Å2
L1.3832 °2-0.1546 °20.1063 °2-1.1508 °2-0.3846 °2--2.2219 °2
S0.0608 Å °-0.0036 Å °-0.048 Å °-0.0142 Å °0.0584 Å °0.0251 Å °-0.0234 Å °0.0384 Å °-0.1105 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 301
2X-RAY DIFFRACTION1allB1 - 26
3X-RAY DIFFRACTION1allC1 - 26
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allE1 - 36
6X-RAY DIFFRACTION1allF1

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