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- PDB-8vmw: Homing endonuclease I-PpoI-DNA complex:ground state at pH6.0 (K+ ... -

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Basic information

Entry
Database: PDB / ID: 8vmw
TitleHoming endonuclease I-PpoI-DNA complex:ground state at pH6.0 (K+ MES) with Na+
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: 1.6 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)49,00315
Polymers48,2344
Non-polymers76811
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-87 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.880, 113.880, 88.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 , 4 types, 391 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
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: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.6→49.31 Å / Num. obs: 168718 / % possible obs: 99.7 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.07 / Net I/σ(I): 15.46
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.690.707272550.7640.7931
1.69-1.810.428256780.9080.4771
1.81-1.950.276237380.9530.3111
1.95-2.140.15220500.9860.1661
2.14-2.390.095198940.9940.1051
2.39-2.760.062175060.9970.0691
2.76-3.380.041148240.9990.0451
3.38-4.770.031114510.9990.0341
4.77-49.310.02863220.9990.0311

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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: 1.6→49.31 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 4333 4.98 %
Rwork0.184 --
obs0.1847 87080 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 854 36 380 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083564
X-RAY DIFFRACTIONf_angle_d1.1115040
X-RAY DIFFRACTIONf_dihedral_angle_d19.8091327
X-RAY DIFFRACTIONf_chiral_restr0.07545
X-RAY DIFFRACTIONf_plane_restr0.008511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.25281460.22892698X-RAY DIFFRACTION97
1.62-1.640.25281630.20872700X-RAY DIFFRACTION100
1.64-1.660.26131420.20392740X-RAY DIFFRACTION100
1.66-1.680.20881480.20282729X-RAY DIFFRACTION100
1.68-1.70.21731550.19522715X-RAY DIFFRACTION100
1.7-1.720.18791420.18522731X-RAY DIFFRACTION100
1.72-1.750.21031610.18792714X-RAY DIFFRACTION100
1.75-1.770.20231260.18972763X-RAY DIFFRACTION100
1.77-1.80.24991620.22762X-RAY DIFFRACTION100
1.8-1.830.2811140.22552730X-RAY DIFFRACTION100
1.83-1.860.19361280.21252748X-RAY DIFFRACTION100
1.86-1.90.21581530.20972771X-RAY DIFFRACTION100
1.9-1.930.20921380.2022685X-RAY DIFFRACTION99
1.93-1.970.2191210.19782808X-RAY DIFFRACTION100
1.97-2.010.18971400.18342729X-RAY DIFFRACTION100
2.01-2.060.20511570.19292734X-RAY DIFFRACTION100
2.06-2.110.22521210.18592762X-RAY DIFFRACTION100
2.11-2.170.18371460.19172729X-RAY DIFFRACTION100
2.17-2.230.22021570.19372782X-RAY DIFFRACTION100
2.23-2.310.22641390.19892759X-RAY DIFFRACTION100
2.31-2.390.21081450.19452734X-RAY DIFFRACTION100
2.39-2.480.21871540.19872796X-RAY DIFFRACTION100
2.48-2.60.19921510.22771X-RAY DIFFRACTION100
2.6-2.730.19281240.20192749X-RAY DIFFRACTION99
2.73-2.910.2431480.20272764X-RAY DIFFRACTION100
2.91-3.130.21251520.19962791X-RAY DIFFRACTION100
3.13-3.440.18591530.17772788X-RAY DIFFRACTION100
3.45-3.940.18521340.16612812X-RAY DIFFRACTION100
3.94-4.970.1421760.1382808X-RAY DIFFRACTION100
4.97-49.310.1521370.14442945X-RAY DIFFRACTION100

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