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- PDB-2ex5: Group I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA -

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Basic information

Entry
Database: PDB / ID: 2ex5
TitleGroup I Intron-encoded Homing Endonuclease I-CeuI Complexed With DNA
Components
  • DNA endonuclease I-CeuI
  • I-CeuI DNA target site
  • I-CeuI DNA target site, complementary strand
KeywordsHydrolase/DNA / homing endonuclease / LAGLIDADG / homodimer / protein-DNA complex / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / 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
DNA / DNA (> 10) / DNA endonuclease I-CeuI
Similarity search - Component
Biological speciesChlamydomonas eugametos (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSpiegel, P.C. / Stoddard, B.L.
CitationJournal: Structure / Year: 2006
Title: The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold.
Authors: Spiegel, P.C. / Chevalier, B. / Sussman, D. / Turmel, M. / Lemieux, C. / Stoddard, B.L.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 30, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn
Item: _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: I-CeuI DNA target site
Y: I-CeuI DNA target site, complementary strand
A: DNA endonuclease I-CeuI
B: DNA endonuclease I-CeuI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3797
Polymers63,2594
Non-polymers1203
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.234, 69.176, 169.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain I-CeuI DNA target site


Mass: 8046.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized nucleic acid / Source: (synth.) synthetic construct (others)
#2: DNA chain I-CeuI DNA target site, complementary strand


Mass: 7930.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized nucleic acid / Source: (synth.) synthetic construct (others)
#3: Protein DNA endonuclease I-CeuI / 23S rRNA intron 1 protein


Mass: 23641.180 Da / Num. of mol.: 2 / Mutation: Q93R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas eugametos (plant) / Gene: I-CeuI / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P32761, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26-36% (v:v) PEG 400, 100 mM TrisHCl, 100 mM KCl, 10 mM CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
126-36% (v:v) PEG 40011
2100 mM TrisHCl11
3100 mM KCl11
410 mM CaCl211
526-36% (v:v) PEG 40012
6100 mM KCl12
710 mM CaCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 30829 / Num. obs: 29588 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.078 / Net I/σ(I): 25.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: molecular replacement was performed with a starting model generated from the lower resolution MAD phases.

Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2959 9.6 %RANDOM
Rwork0.219 ---
all0.219 30829 --
obs0.219 29588 96 %-
Solvent computationBsol: 39.28 Å2
Displacement parametersBiso mean: 43.599 Å2
Baniso -1Baniso -2Baniso -3
1--2.416 Å20 Å20 Å2
2---9.582 Å20 Å2
3---11.998 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 1060 3 263 4664
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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