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- PDB-3e54: Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed W... -

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Basic information

Entry
Database: PDB / ID: 3.0E+54
TitleArchaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA
Components
  • DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')
  • DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')
  • DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')
  • DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')
  • RRNA intron-encoded endonuclease
KeywordsHYDROLASE/DNA / protein-DNA complex / LAGLIDADG / homing / endonuclease / DNA recognition / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


endonuclease activity / metal ion binding
Similarity search - Function
: / LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ETHANOL / DNA / DNA (> 10) / rRNA intron-encoded endonuclease
Similarity search - Component
Biological speciesVulcanisaeta distributa (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsNomura, N. / Nomura, Y. / Sussman, D. / Stoddard, B.L.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases
Authors: Nomura, N. / Nomura, Y. / Sussman, D. / Klein, D. / Stoddard, B.L.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 12, 2014Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRNA intron-encoded endonuclease
B: RRNA intron-encoded endonuclease
C: DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')
D: DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')
E: DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')
F: DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90614
Polymers52,6466
Non-polymers2608
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-106 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.580, 66.580, 217.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RRNA intron-encoded endonuclease / Homing Endonuclease I-Vdi141I


Mass: 19616.646 Da / Num. of mol.: 2 / Mutation: I65M, I107M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vulcanisaeta distributa (archaea) / Strain: IC-141 / Gene: 23S rRNA intron (Vdi141.L1927) / Plasmid: pVdiI65M/I107M-10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q6L703, Hydrolases; Acting on ester bonds

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DNA chain , 4 types, 4 molecules CDEF

#2: DNA chain DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3')


Mass: 3901.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: I-Vdi141I DNA Target Site
#3: DNA chain DNA (5'-D(P*DGP*DGP*DTP*DAP*DGP*DCP*DCP*DAP*DA)-3')


Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: I-Vdi141I DNA Target Site
#4: DNA chain DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3')


Mass: 3941.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: I-Vdi141I DNA Target Site
#5: DNA chain DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3')


Mass: 2804.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: I-Vdi141I DNA Target Site

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Non-polymers , 3 types, 121 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9% ethanol, 100mM MgCl2, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 299K
Components of the solutions
IDNameCrystal-IDSol-ID
1ethanol11
2MgCl211
3HEPES-NaOH11
4H2O11
5MgCl212
6HEPES-NaOH12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97911, 0.97945
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979451
ReflectionResolution: 2.32→50 Å / Num. obs: 23652 / % possible obs: 99.4 % / Redundancy: 22.4 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.252 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→45.16 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2019520.67 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1798 9.9 %RANDOM
Rwork0.231 ---
obs0.231 18252 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9873 Å2 / ksol: 0.335746 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å2-1.58 Å20 Å2
2--6.13 Å20 Å2
3----12.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 898 14 113 3635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.281.5
X-RAY DIFFRACTIONc_mcangle_it5.832
X-RAY DIFFRACTIONc_scbond_it6.232
X-RAY DIFFRACTIONc_scangle_it8.072.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 310 10.5 %
Rwork0.309 2645 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5EtOH.paramEtOH.top

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