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- PDB-8vmp: Homing endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES)... -

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Basic information

Entry
Database: PDB / ID: 8vmp
TitleHoming endonuclease I-PpoI-DNA complex:reaction at pH7.0 (K+ MES) with 500 uM Mg2+ for 10s
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: 1.45 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
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13240 Å2
ΔGint-85 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.580, 113.580, 87.990
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-741-

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 , 4 types, 409 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.: 398 / 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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Malonate, PEG 3350, 0.1 M MES

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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: Mar 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.45→42.93 Å / Num. obs: 224615 / % possible obs: 99.2 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.09 / Net I/σ(I): 10.01
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.45-1.540.617356340.7690.7031
1.54-1.640.377343650.9120.4251
1.64-1.770.227320630.9640.2561
1.77-1.940.158295100.9780.1791
1.94-2.170.11265090.9870.1241
2.17-2.50.087234780.9910.0981
2.5-3.070.072196610.9940.0811
3.07-4.330.06151100.9950.0681
4.33-42.930.04882850.9960.0541

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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: 1.45→42.93 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 5775 5 %
Rwork0.1793 --
obs0.1796 115462 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 854 36 398 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083558
X-RAY DIFFRACTIONf_angle_d1.0675030
X-RAY DIFFRACTIONf_dihedral_angle_d19.9951323
X-RAY DIFFRACTIONf_chiral_restr0.076544
X-RAY DIFFRACTIONf_plane_restr0.008509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.460.26831750.23513135X-RAY DIFFRACTION85
1.46-1.480.22182000.22333629X-RAY DIFFRACTION100
1.48-1.50.21321780.21783681X-RAY DIFFRACTION100
1.5-1.520.22151810.20593661X-RAY DIFFRACTION100
1.52-1.540.23111570.21313679X-RAY DIFFRACTION100
1.54-1.560.24471760.20133660X-RAY DIFFRACTION100
1.56-1.580.20182390.1973669X-RAY DIFFRACTION100
1.58-1.60.21872110.19753605X-RAY DIFFRACTION100
1.6-1.630.20431960.17743670X-RAY DIFFRACTION100
1.63-1.660.18662090.17123625X-RAY DIFFRACTION100
1.66-1.690.21822030.17273657X-RAY DIFFRACTION100
1.69-1.720.17111930.16323706X-RAY DIFFRACTION100
1.72-1.750.17041720.16763666X-RAY DIFFRACTION100
1.75-1.780.21671690.1773643X-RAY DIFFRACTION100
1.78-1.820.1821850.17773725X-RAY DIFFRACTION100
1.82-1.870.16931830.18483697X-RAY DIFFRACTION100
1.87-1.910.19841920.19273678X-RAY DIFFRACTION100
1.91-1.960.20151660.19363669X-RAY DIFFRACTION100
1.96-2.020.19322160.18523671X-RAY DIFFRACTION100
2.02-2.090.16551890.18943677X-RAY DIFFRACTION100
2.09-2.160.2031690.18623719X-RAY DIFFRACTION100
2.16-2.250.21942050.18463646X-RAY DIFFRACTION100
2.25-2.350.19472030.18693676X-RAY DIFFRACTION100
2.35-2.470.21471970.19183687X-RAY DIFFRACTION99
2.47-2.630.18261960.1973672X-RAY DIFFRACTION99
2.63-2.830.18661760.19783710X-RAY DIFFRACTION99
2.83-3.120.2071900.1973680X-RAY DIFFRACTION99
3.12-3.570.16912300.18163650X-RAY DIFFRACTION98
3.57-4.490.15572050.15093690X-RAY DIFFRACTION98
4.5-42.930.15762140.14013754X-RAY DIFFRACTION97

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