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

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Basic information

Entry
Database: PDB / ID: 12fk
TitleAncestral Reconstruction of a Homing Endonuclease
Components
  • DNA (5'-D(P*GP*AP*AP*CP*CP*TP*TP*TP*GP*GP*TP*TP*AP*TP*GP*AP*GP*GP*AP*TP*CP*TP*TP*C)-3')
  • DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*CP*CP*TP*CP*AP*TP*AP*AP*CP*CP*AP*AP*AP*GP*GP*TP*T)-3')
  • aHE31
KeywordsDNA BINDING PROTEIN / Reconstruction / Evolution
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 2, 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

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Assembly

Deposited unit
A: aHE31
B: DNA (5'-D(P*GP*AP*AP*CP*CP*TP*TP*TP*GP*GP*TP*TP*AP*TP*GP*AP*GP*GP*AP*TP*CP*TP*TP*C)-3')
C: DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*CP*CP*TP*CP*AP*TP*AP*AP*CP*CP*AP*AP*AP*GP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7355
Polymers49,6553
Non-polymers802
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-83 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.453, 47.371, 74.737
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein aHE31


Mass: 34917.215 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 (5'-D(P*GP*AP*AP*CP*CP*TP*TP*TP*GP*GP*TP*TP*AP*TP*GP*AP*GP*GP*AP*TP*CP*TP*TP*C)-3')


Mass: 7390.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*CP*CP*TP*CP*AP*TP*AP*AP*CP*CP*AP*AP*AP*GP*GP*TP*T)-3')


Mass: 7346.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: 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.: 301 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.2 Ammonium sulfate, 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: 5.0.2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.17→47.37 Å / Num. obs: 21419 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.109 / Rrim(I) all: 0.28 / Χ2: 1.05 / Net I/σ(I): 6.2 / Num. measured all: 140336
Reflection shellResolution: 2.17→2.24 Å / % possible obs: 96.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.031 / Num. measured all: 11340 / Num. unique obs: 1790 / CC1/2: 0.689 / Rpim(I) all: 0.44 / Rrim(I) all: 1.124 / Χ2: 0.98 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
Aimless0.7.4data scaling
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→42.52 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 2134 10 %
Rwork0.2307 --
obs0.2363 21331 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 984 2 301 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043563
X-RAY DIFFRACTIONf_angle_d0.6245033
X-RAY DIFFRACTIONf_dihedral_angle_d23.4061439
X-RAY DIFFRACTIONf_chiral_restr0.041569
X-RAY DIFFRACTIONf_plane_restr0.004471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.220.39111360.30541227X-RAY DIFFRACTION96
2.22-2.280.3751440.30131289X-RAY DIFFRACTION99
2.28-2.340.39421440.28051289X-RAY DIFFRACTION99
2.34-2.410.33691380.27951231X-RAY DIFFRACTION99
2.41-2.480.34681470.2661318X-RAY DIFFRACTION100
2.48-2.570.37831390.27051263X-RAY DIFFRACTION99
2.57-2.680.32971430.25191283X-RAY DIFFRACTION97
2.68-2.80.31261380.2571261X-RAY DIFFRACTION98
2.8-2.940.3011430.25371279X-RAY DIFFRACTION99
2.95-3.130.29511430.23211286X-RAY DIFFRACTION99
3.13-3.370.28181410.21061275X-RAY DIFFRACTION98
3.37-3.710.21481420.18651272X-RAY DIFFRACTION97
3.71-4.250.22311420.19251284X-RAY DIFFRACTION99
4.25-5.350.23361450.18971306X-RAY DIFFRACTION98
5.35-42.520.25941490.22731334X-RAY DIFFRACTION99

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