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- PDB-8vnf: Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES)... -

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Basic information

Entry
Database: PDB / ID: 8vnf
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 20s
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: 1.5 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

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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)49,11217
Polymers48,2344
Non-polymers87813
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-101 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.060, 114.060, 88.020
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-751-

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, 414 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#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.: 401 / 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: 3.43 Å3/Da / Density % sol: 64.1 %
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: 0.9765 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.5→43.07 Å / Num. obs: 205799 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.084 / Net I/σ(I): 12.04
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.590.933331060.7241.0311
1.59-1.70.487313270.9090.5371
1.7-1.830.268291210.9670.2951
1.83-2.010.164267870.9850.1811
2.01-2.250.107242810.9920.1181
2.25-2.590.082214090.9940.091
2.59-3.170.064180790.9960.0711
3.17-4.480.051139720.9970.0561
4.48-43.070.04177170.9980.0451

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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: 1.5→43.07 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 5413 5.11 %
Rwork0.1816 --
obs0.1823 105906 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 38 401 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013658
X-RAY DIFFRACTIONf_angle_d1.2285188
X-RAY DIFFRACTIONf_dihedral_angle_d19.761363
X-RAY DIFFRACTIONf_chiral_restr0.092560
X-RAY DIFFRACTIONf_plane_restr0.007513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.31571730.27453232X-RAY DIFFRACTION98
1.52-1.530.23631840.25263351X-RAY DIFFRACTION100
1.53-1.550.24351710.23083278X-RAY DIFFRACTION100
1.55-1.570.23571920.22393333X-RAY DIFFRACTION100
1.57-1.590.20061750.21263309X-RAY DIFFRACTION100
1.59-1.610.23522050.20473309X-RAY DIFFRACTION100
1.61-1.640.22041820.19173372X-RAY DIFFRACTION100
1.64-1.660.19912000.18533258X-RAY DIFFRACTION100
1.66-1.690.22711870.18563319X-RAY DIFFRACTION100
1.69-1.710.19271770.17543353X-RAY DIFFRACTION100
1.71-1.740.20571700.17843321X-RAY DIFFRACTION100
1.74-1.780.19571710.18243369X-RAY DIFFRACTION100
1.78-1.810.18621970.18983300X-RAY DIFFRACTION100
1.81-1.850.2191710.19383343X-RAY DIFFRACTION100
1.85-1.890.22082010.19813312X-RAY DIFFRACTION100
1.89-1.930.21441840.2023342X-RAY DIFFRACTION100
1.93-1.980.21512040.19793299X-RAY DIFFRACTION100
1.98-2.030.20562210.18793322X-RAY DIFFRACTION100
2.03-2.090.20391780.1943337X-RAY DIFFRACTION100
2.09-2.160.20751690.18813350X-RAY DIFFRACTION100
2.16-2.240.1861540.18713371X-RAY DIFFRACTION100
2.24-2.330.1982110.18783360X-RAY DIFFRACTION100
2.33-2.430.20331490.19353377X-RAY DIFFRACTION100
2.43-2.560.21741890.19093342X-RAY DIFFRACTION100
2.56-2.720.20111650.19763405X-RAY DIFFRACTION100
2.72-2.930.19421860.19773371X-RAY DIFFRACTION100
2.93-3.230.20441500.19783403X-RAY DIFFRACTION100
3.23-3.690.2071700.1783423X-RAY DIFFRACTION100
3.69-4.650.14281730.14353451X-RAY DIFFRACTION100
4.65-43.070.15661540.1393581X-RAY DIFFRACTION100

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