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- PDB-12hh: Ancestral Reconstruction of a Homing Endonuclease -

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Basic information

Entry
Database: PDB / ID: 12hh
TitleAncestral Reconstruction of a Homing Endonuclease
Components
  • (DNA (26-MER)) x 2
  • aHE15
KeywordsDNA BINDING PROTEIN / Reconstruction / Evolution
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsDoyle, L.A. / Stoddard, B. / Young, J.C. / Silverstein, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM148166 United States
CitationJournal: To Be Published
Title: Ancestral Homing Endonuclease reconstructions
Authors: Stoddard, B.
History
DepositionApr 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aHE15
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6015
Polymers49,5213
Non-polymers802
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-73 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.891, 54.040, 164.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein aHE15


Mass: 33546.750 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)
#2: DNA chain DNA (26-MER)


Mass: 7956.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8018.177 Da / Num. of mol.: 1 / 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.: 63 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM HEPES pH7.5, 150 mM NaCl, 28% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.37→45.19 Å / Num. obs: 18776 / % possible obs: 92.7 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Χ2: 0.93 / Net I/σ(I): 19.1 / Num. measured all: 226427
Reflection shellResolution: 2.37→2.46 Å / % possible obs: 61.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.674 / Num. measured all: 10686 / Num. unique obs: 1268 / CC1/2: 0.881 / Rpim(I) all: 0.232 / Rrim(I) all: 0.717 / Χ2: 0.59 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
Aimless0.7.13data scaling
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→45.19 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 33.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 1773 10 %
Rwork0.2307 --
obs0.2355 17726 87.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 1060 2 63 3401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043512
X-RAY DIFFRACTIONf_angle_d0.5944977
X-RAY DIFFRACTIONf_dihedral_angle_d24.1731402
X-RAY DIFFRACTIONf_chiral_restr0.039565
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.404760.3601698X-RAY DIFFRACTION51
2.43-2.510.4666920.3324825X-RAY DIFFRACTION61
2.51-2.590.3421190.3211045X-RAY DIFFRACTION75
2.59-2.680.36721260.2981137X-RAY DIFFRACTION83
2.68-2.790.35011260.30471212X-RAY DIFFRACTION88
2.79-2.910.3511430.29261272X-RAY DIFFRACTION92
2.91-3.070.39751420.31411318X-RAY DIFFRACTION94
3.07-3.260.33451470.25041345X-RAY DIFFRACTION96
3.26-3.510.27981580.23481360X-RAY DIFFRACTION97
3.51-3.860.28821570.21791399X-RAY DIFFRACTION98
3.86-4.420.22811570.19121377X-RAY DIFFRACTION99
4.42-5.570.23761600.18251437X-RAY DIFFRACTION99
5.57-45.190.20321700.19641528X-RAY DIFFRACTION100

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