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

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Basic information

Entry
Database: PDB / ID: 8vnb
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH8.0 (Tris) with 500 uM Mg2+ for 240s
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: 1.72 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
CitationJournal: To Be Published
Title: Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s
Authors: Chang, C. / 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

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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 area13810 Å2
ΔGint-76 kcal/mol
Surface area18520 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-724-

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

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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: 1.72→42.99 Å / Num. obs: 136475 / % possible obs: 99.5 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.109 / Net I/σ(I): 10.27
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.72-1.820.82214620.740.9061
1.82-1.950.533208590.8840.5871
1.95-2.10.314194130.9510.3461
2.1-2.30.206178380.9760.2271
2.3-2.570.145161950.9870.161
2.57-2.970.102141670.9920.1121
2.97-3.640.07120690.9960.0781
3.64-5.130.05793210.9970.0621
5.13-42.990.04551510.9980.0491

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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: 1.72→42.99 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 3554 5.06 %
Rwork0.1772 --
obs0.1782 70226 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→42.99 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_d1.1625019
X-RAY DIFFRACTIONf_dihedral_angle_d19.8361314
X-RAY DIFFRACTIONf_chiral_restr0.079542
X-RAY DIFFRACTIONf_plane_restr0.011508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.26991710.22662545X-RAY DIFFRACTION98
1.74-1.770.22141330.21362649X-RAY DIFFRACTION100
1.77-1.790.24161260.22142645X-RAY DIFFRACTION100
1.79-1.820.22861200.20392667X-RAY DIFFRACTION100
1.82-1.850.27021360.20432608X-RAY DIFFRACTION100
1.85-1.880.22431460.19542655X-RAY DIFFRACTION100
1.88-1.920.22481360.20112693X-RAY DIFFRACTION100
1.92-1.950.24371540.19942600X-RAY DIFFRACTION100
1.95-1.990.23281190.19922701X-RAY DIFFRACTION100
1.99-2.040.21381430.19142656X-RAY DIFFRACTION100
2.04-2.080.21711430.17542628X-RAY DIFFRACTION100
2.08-2.140.18751400.18182654X-RAY DIFFRACTION100
2.14-2.190.20681130.18072686X-RAY DIFFRACTION100
2.19-2.260.22641480.18212659X-RAY DIFFRACTION100
2.26-2.330.19341560.1872638X-RAY DIFFRACTION100
2.33-2.410.20211750.18922638X-RAY DIFFRACTION100
2.42-2.510.20221610.19382646X-RAY DIFFRACTION100
2.51-2.630.23191340.19972682X-RAY DIFFRACTION100
2.63-2.760.2081660.1982666X-RAY DIFFRACTION100
2.76-2.940.2171380.19652680X-RAY DIFFRACTION100
2.94-3.160.2311510.19612675X-RAY DIFFRACTION100
3.16-3.480.17961210.17562717X-RAY DIFFRACTION100
3.48-3.990.16241600.15772683X-RAY DIFFRACTION100
3.99-5.020.15741140.13052757X-RAY DIFFRACTION100
5.02-42.990.1511500.14482844X-RAY DIFFRACTION100

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