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

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Basic information

Entry
Database: PDB / ID: 8vnc
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 320s
Components
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • Intron-encoded endonuclease I-PpoI
KeywordsHYDROLASE/DNA / Intron encoded homing endonuclease I-PpoI / HYDROLASE / HYDROLASE-DNA complex
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: 1.62 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 1.1Jul 17, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 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 1.3Jan 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*A)-3')
c: DNA (5'-D(P*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*A)-3')
d: DNA (5'-D(P*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)48,91517
Polymers48,1456
Non-polymers77111
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-75 kcal/mol
Surface area18510 Å2
MethodPISA
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-720-

HOH

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Components

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DNA chain , 2 types, 4 molecules CDcd

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


Mass: 3916.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')


Mass: 2475.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#3: 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 , 4 types, 408 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 1.62→47.79 Å / Num. obs: 162716 / % possible obs: 99.7 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.089 / Net I/σ(I): 11.74
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.62-1.720.811258700.7430.8961
1.72-1.840.502248070.8880.5541
1.84-1.990.298230500.9580.3281
1.99-2.180.174212750.9830.1921
2.18-2.430.121192360.9910.1331
2.43-2.810.087169210.9940.0961
2.81-3.440.062143490.9970.0691
3.44-4.850.049110680.9980.0541
4.85-47.790.03861390.9980.0421

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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: 1.62→47.79 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1883 4235 5.09 %
Rwork0.1797 --
obs0.1801 83212 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 36 397 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093553
X-RAY DIFFRACTIONf_angle_d1.1595019
X-RAY DIFFRACTIONf_dihedral_angle_d19.7291314
X-RAY DIFFRACTIONf_chiral_restr0.079542
X-RAY DIFFRACTIONf_plane_restr0.01508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.25071370.242595X-RAY DIFFRACTION100
1.64-1.660.24741160.2332618X-RAY DIFFRACTION100
1.66-1.680.25581470.21952591X-RAY DIFFRACTION100
1.68-1.70.23721430.21312615X-RAY DIFFRACTION100
1.7-1.720.21641330.19622622X-RAY DIFFRACTION100
1.72-1.750.18261060.19192637X-RAY DIFFRACTION100
1.75-1.770.23671490.19922615X-RAY DIFFRACTION100
1.77-1.80.22281500.19792609X-RAY DIFFRACTION100
1.8-1.830.18571540.19092594X-RAY DIFFRACTION100
1.83-1.860.19471310.19532595X-RAY DIFFRACTION100
1.86-1.890.21851470.19022636X-RAY DIFFRACTION100
1.89-1.920.23561130.19762644X-RAY DIFFRACTION100
1.92-1.960.21741680.20132586X-RAY DIFFRACTION100
1.96-20.20321190.19162653X-RAY DIFFRACTION100
2-2.040.19361410.18952576X-RAY DIFFRACTION100
2.04-2.090.20511620.18342601X-RAY DIFFRACTION100
2.09-2.140.19151520.18352651X-RAY DIFFRACTION100
2.14-2.20.18311290.19052610X-RAY DIFFRACTION100
2.2-2.270.20361300.18812640X-RAY DIFFRACTION100
2.27-2.340.23161410.19132638X-RAY DIFFRACTION100
2.34-2.420.2161450.19422632X-RAY DIFFRACTION100
2.42-2.520.20491320.20082645X-RAY DIFFRACTION100
2.52-2.640.21151690.2032596X-RAY DIFFRACTION100
2.64-2.780.19841260.19572676X-RAY DIFFRACTION100
2.78-2.950.18961150.19642664X-RAY DIFFRACTION100
2.95-3.180.19981360.19912668X-RAY DIFFRACTION100
3.18-3.50.18461450.1722646X-RAY DIFFRACTION100
3.5-40.17871540.16062683X-RAY DIFFRACTION100
4-5.040.13911700.13062656X-RAY DIFFRACTION100
5.04-47.790.14291750.14422785X-RAY DIFFRACTION100

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