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- PDB-8vn8: Homing endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) w... -

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Basic information

Entry
Database: PDB / ID: 8vn8
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 40s
Components
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • Intron-encoded endonuclease I-PpoI
KeywordsHYDROLASE / Intron encoded homing endonuclease I-PpoI
Function / homology
Function and homology information


intron homing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Zinc-binding loop region of homing endonuclease / Homing endonuclease, His-Me finger superfamily / Zinc-binding loop region of homing endonuclease / His-Me finger superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Intron-encoded endonuclease I-PpoI
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChang, C. / Gao, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR190046 United States
Welch FoundationC-2033-20200401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008280 United States
Citation
Journal: Elife / Year: 2024
Title: Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo.
Authors: Chang, C. / Zhou, G. / Gao, Y.
#1: Journal: Elife / Year: 2024
Title: Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo
Authors: Chang, C. / Zhou, G. / Gao, Y.
History
DepositionJan 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 29, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')
D: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')
A: Intron-encoded endonuclease I-PpoI
B: Intron-encoded endonuclease I-PpoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,05117
Polymers48,2344
Non-polymers81713
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.650, 113.650, 88.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

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Components

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DNA chain / Protein , 2 types, 4 molecules CDAB

#1: DNA chain DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')


Mass: 6437.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Intron-encoded endonuclease I-PpoI / I-Ppo


Mass: 17680.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q94702, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 413 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Sodium Malonate, PEG 3350, 0.1 M MES / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.6→47.79 Å / Num. obs: 167997 / % possible obs: 99.7 % / Redundancy: 11 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.53
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.859

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.79 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 4312 4.98 %
Rwork0.178 --
obs0.179 86625 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 854 38 400 3782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093663
X-RAY DIFFRACTIONf_angle_d1.1555197
X-RAY DIFFRACTIONf_dihedral_angle_d19.6861366
X-RAY DIFFRACTIONf_chiral_restr0.086562
X-RAY DIFFRACTIONf_plane_restr0.009514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.24631300.25072405X-RAY DIFFRACTION89
1.62-1.640.25921610.22632713X-RAY DIFFRACTION100
1.64-1.660.26421400.21732710X-RAY DIFFRACTION100
1.66-1.680.211580.20692726X-RAY DIFFRACTION100
1.68-1.70.20211580.20352711X-RAY DIFFRACTION100
1.7-1.720.22131390.1912724X-RAY DIFFRACTION100
1.72-1.750.22341550.19152703X-RAY DIFFRACTION100
1.75-1.770.23361310.19352775X-RAY DIFFRACTION100
1.77-1.80.20691580.1912725X-RAY DIFFRACTION100
1.8-1.830.23031100.19362753X-RAY DIFFRACTION100
1.83-1.860.20931370.1952744X-RAY DIFFRACTION100
1.86-1.90.19761480.2052746X-RAY DIFFRACTION100
1.9-1.930.1961360.19312721X-RAY DIFFRACTION100
1.93-1.970.22561180.19342790X-RAY DIFFRACTION100
1.97-2.010.18091480.18382727X-RAY DIFFRACTION100
2.01-2.060.21831560.19092729X-RAY DIFFRACTION100
2.06-2.110.19931150.18152770X-RAY DIFFRACTION100
2.11-2.170.20381520.1882722X-RAY DIFFRACTION100
2.17-2.230.23611480.18832754X-RAY DIFFRACTION100
2.23-2.310.22181400.19372745X-RAY DIFFRACTION100
2.31-2.390.20731500.19582769X-RAY DIFFRACTION100
2.39-2.480.20431560.19572732X-RAY DIFFRACTION100
2.48-2.60.20351470.1982773X-RAY DIFFRACTION100
2.6-2.730.20971280.19862763X-RAY DIFFRACTION100
2.73-2.910.2161450.19452787X-RAY DIFFRACTION100
2.91-3.130.21491470.19622775X-RAY DIFFRACTION100
3.13-3.440.17731550.17332767X-RAY DIFFRACTION100
3.45-3.940.20261320.1612807X-RAY DIFFRACTION100
3.94-4.970.13291760.12762807X-RAY DIFFRACTION100
4.97-47.790.14321380.14132940X-RAY DIFFRACTION100

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