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- PDB-2i3p: K28R mutant of Homing Endonuclease I-CreI -

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Basic information

Entry
Database: PDB / ID: 2i3p
TitleK28R mutant of Homing Endonuclease I-CreI
Components
  • 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3'
  • DNA endonuclease I-CreI
KeywordsHYDROLASE/DNA / Homing endonulease I-CreI / DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein 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-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSussman, D. / Rosen, L.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Homing endonuclease I-CreI derivatives with novel DNA target specificities.
Authors: Rosen, L.E. / Morrison, H.A. / Masri, S. / Brown, M.J. / Springstubb, B. / Sussman, D. / Stoddard, B.L. / Seligman, L.M.
History
DepositionAug 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 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.name
Revision 1.4Oct 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.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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3'
D: 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3'
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1696
Polymers50,0894
Non-polymers802
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.076, 68.211, 87.409
Angle α, β, γ (deg.)90.000, 91.420, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe assymetric unit contains one biologically active complex. I-CreI binds the DNA substrate as a homodimer and subsequently cleaves both strands.

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Components

#1: DNA chain 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3'


Mass: 7393.792 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3'


Mass: 7344.753 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA endonuclease I-CreI / 23S rRNA intron protein


Mass: 17675.328 Da / Num. of mol.: 2 / Mutation: K28R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pI-CreI / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 RIL
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG 400 28%, pH 6.5, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2HOH11
3PEG 40012
4HOH12

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→27.69 Å / Num. obs: 21742 / % possible obs: 96 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.039 / Χ2: 1.462 / Net I/σ(I): 26.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.097 / Num. unique all: 1033 / Χ2: 1.424 / % possible all: 93.9

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Phasing

Phasing MRRfactor: 0.398 / Cor.coef. Fo:Fc: 0.608
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
EPMR2.5phasing
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9Y
Resolution: 2.3→27.69 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.292 2137 9.4 %
Rwork0.234 --
obs-21471 94.8 %
Solvent computationBsol: 38.114 Å2
Displacement parametersBiso mean: 24.169 Å2
Baniso -1Baniso -2Baniso -3
1--2.707 Å20 Å21.167 Å2
2--3.255 Å20 Å2
3----0.548 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 978 2 221 3679
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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