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- PDB-2i3q: Q44V mutant of Homing Endonuclease I-CreI -

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Basic information

Entry
Database: PDB / ID: 2i3q
TitleQ44V mutant of Homing Endonuclease I-CreI
Components
  • 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*TP*TP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP*GP*TP*TP*TP*CP*G)-3'
  • DNA endonuclease I-CreI
KeywordsHYDROLASE/DNA / Homing Endonuclease / I-CreI / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein 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-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRosen, L. / Sussman, D.
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.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 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

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Assembly

Deposited unit
C: 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP*GP*TP*TP*TP*CP*G)-3'
D: 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*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)49,9406
Polymers49,8604
Non-polymers802
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.060, 67.978, 87.497
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe assymetric unit contains one biologically active unit. A homodimer of I-CreI and a DNA duplex substrate

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Components

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


Mass: 7418.804 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*TP*TP*TP*GP*C)-3'


Mass: 7320.728 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA endonuclease I-CreI / 23S rRNA intron protein


Mass: 17560.215 Da / Num. of mol.: 2 / Mutation: Q44V
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.: 147 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
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 II / 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: 19300 / % possible obs: 85.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.039 / Χ2: 1.293 / Net I/σ(I): 21.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.341.60.0918861.48980.5
2.34-2.381.80.0919681.54685.7
2.38-2.4320.08210051.49388.5
2.43-2.482.20.0829821.32689.3
2.48-2.532.20.07410401.28489.9
2.53-2.592.30.0699721.2689.1
2.59-2.652.30.06610051.28188.9
2.65-2.732.30.0610011.28288.9
2.73-2.812.40.0569911.21588.5
2.81-2.92.40.05310001.28987.3
2.9-32.40.0499591.31487.5
3-3.122.40.0469921.41787.2
3.12-3.262.40.0459691.39985.7
3.26-3.432.40.0389581.42285.5
3.43-3.652.50.0389681.40584
3.65-3.932.50.0369421.37183.7
3.93-4.332.50.0329351.26182.9
4.33-4.952.60.0319221.1181.3
4.95-6.232.60.0319261.11279.7
6.23-302.60.0238790.90975.3

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Phasing

Phasing MRRfactor: 0.394 / Cor.coef. Fo:Fc: 0.638
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9Y

1g9y


Resolution: 2.3→27.69 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.264 1886 8.3 %
Rwork0.217 --
obs-19130 84.7 %
Solvent computationBsol: 33.168 Å2
Displacement parametersBiso mean: 24.066 Å2
Baniso -1Baniso -2Baniso -3
1--5.991 Å20 Å22.224 Å2
2--1.707 Å20 Å2
3---4.284 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 978 2 147 3589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.258
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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