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

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Basic information

Entry
Database: PDB / ID: 8vnh
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 80s
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: 1.76 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)49,11217
Polymers48,2344
Non-polymers87813
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-100 kcal/mol
Surface area18920 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-767-

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-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.: 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: 3.43 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: 1.76→49.39 Å / Num. obs: 126673 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.11 / Net I/σ(I): 9.73
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.76-1.860.871204140.740.9611
1.86-1.990.522192320.8890.5761
1.99-2.150.305179130.9550.3361
2.15-2.360.199165560.9790.2191
2.36-2.630.142149020.9880.1561
2.63-3.040.101131600.9930.1121
3.04-3.720.075110990.9950.0821
3.72-5.240.06586200.9960.0711
5.24-49.390.05647770.9960.0621

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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: 1.76→49.39 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 3340 5.1 %
Rwork0.1808 --
obs0.1821 65539 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 38 400 3784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093663
X-RAY DIFFRACTIONf_angle_d1.1295197
X-RAY DIFFRACTIONf_dihedral_angle_d19.7691366
X-RAY DIFFRACTIONf_chiral_restr0.083562
X-RAY DIFFRACTIONf_plane_restr0.008514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.31371370.24452194X-RAY DIFFRACTION86
1.78-1.810.27521600.2322562X-RAY DIFFRACTION100
1.81-1.840.27171850.21972543X-RAY DIFFRACTION100
1.84-1.870.23961430.21642580X-RAY DIFFRACTION100
1.87-1.90.2541520.20762561X-RAY DIFFRACTION100
1.9-1.930.21491360.21682564X-RAY DIFFRACTION100
1.93-1.970.24811310.20782615X-RAY DIFFRACTION100
1.97-2.010.23561080.19182609X-RAY DIFFRACTION100
2.01-2.060.2391360.19382605X-RAY DIFFRACTION100
2.06-2.10.22661360.18782578X-RAY DIFFRACTION100
2.1-2.160.22131230.19432609X-RAY DIFFRACTION100
2.16-2.210.22341190.18492612X-RAY DIFFRACTION100
2.21-2.280.21141440.1912600X-RAY DIFFRACTION100
2.28-2.350.24551140.19532600X-RAY DIFFRACTION100
2.35-2.440.21421680.19422588X-RAY DIFFRACTION100
2.44-2.530.23731520.19882603X-RAY DIFFRACTION100
2.54-2.650.21811530.2042572X-RAY DIFFRACTION100
2.65-2.790.21831200.19432636X-RAY DIFFRACTION100
2.79-2.960.18541120.20522633X-RAY DIFFRACTION100
2.97-3.190.24811110.1962650X-RAY DIFFRACTION100
3.19-3.520.19691380.1732637X-RAY DIFFRACTION100
3.52-4.020.1911480.1612643X-RAY DIFFRACTION100
4.02-5.070.13851570.12712655X-RAY DIFFRACTION100
5.07-49.390.15821570.1422750X-RAY DIFFRACTION100

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