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

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Basic information

Entry
Database: PDB / ID: 8vno
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 600s
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: 1.7 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)49,02319
Polymers48,1456
Non-polymers87813
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-93 kcal/mol
Surface area18580 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-725-

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 , 5 types, 410 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-MN / MANGANESE (II) ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: 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: 3.43 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: 1.7→47.86 Å / Num. obs: 142915 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Net I/σ(I): 13.47
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.7-1.80.877229370.7250.9681
1.8-1.930.52217460.8840.5731
1.93-2.080.282202290.9620.3111
2.08-2.280.17186330.9840.1871
2.28-2.550.113168600.9930.1241
2.55-2.940.075148700.9960.0831
2.94-3.60.051125320.9980.0561
3.6-5.070.0497100.9980.0441
5.07-47.860.03253960.9990.0351

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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: 1.7→47.86 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 3785 5.2 %
Rwork0.1787 --
obs0.1794 72800 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 38 397 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093653
X-RAY DIFFRACTIONf_angle_d1.2065179
X-RAY DIFFRACTIONf_dihedral_angle_d19.9361360
X-RAY DIFFRACTIONf_chiral_restr0.081558
X-RAY DIFFRACTIONf_plane_restr0.007512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.27691740.23682490X-RAY DIFFRACTION100
1.72-1.740.26591630.23142502X-RAY DIFFRACTION100
1.74-1.770.22061330.21162518X-RAY DIFFRACTION100
1.77-1.790.22541320.21232558X-RAY DIFFRACTION100
1.79-1.820.24621210.20642572X-RAY DIFFRACTION100
1.82-1.850.26311300.19982552X-RAY DIFFRACTION100
1.85-1.880.2231170.19332535X-RAY DIFFRACTION100
1.88-1.910.19791600.19712531X-RAY DIFFRACTION100
1.91-1.950.22751260.21052543X-RAY DIFFRACTION100
1.95-1.980.20981200.20312544X-RAY DIFFRACTION100
1.98-2.020.20891240.18852552X-RAY DIFFRACTION100
2.02-2.070.21021360.1842553X-RAY DIFFRACTION100
2.07-2.120.25471480.18042543X-RAY DIFFRACTION100
2.12-2.170.18631570.18522508X-RAY DIFFRACTION100
2.17-2.230.18291240.18582555X-RAY DIFFRACTION100
2.23-2.290.19681650.18892511X-RAY DIFFRACTION100
2.29-2.370.21581330.19052553X-RAY DIFFRACTION100
2.37-2.450.18891370.1952566X-RAY DIFFRACTION100
2.45-2.550.20691490.19812542X-RAY DIFFRACTION100
2.55-2.670.18541540.20052568X-RAY DIFFRACTION100
2.67-2.810.17281230.19112558X-RAY DIFFRACTION100
2.81-2.980.24171310.20122580X-RAY DIFFRACTION100
2.98-3.210.22381390.19852570X-RAY DIFFRACTION100
3.21-3.540.19491500.17512587X-RAY DIFFRACTION100
3.54-4.050.16681230.15592607X-RAY DIFFRACTION100
4.05-5.10.13861460.1252614X-RAY DIFFRACTION100
5.1-47.860.15011700.13892703X-RAY DIFFRACTION100

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