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- PDB-2o7m: The C-terminal loop of the homing endonuclease I-CreI is essentia... -

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Basic information

Entry
Database: PDB / ID: 2o7m
TitleThe C-terminal loop of the homing endonuclease I-CreI is essential for DNA binding and cleavage. Identification of a novel site for specificity engineering in the I-CreI scaffold
ComponentsDNA endonuclease I-CreI
KeywordsHYDROLASE / Homing endonuclease / DNA
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 endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPrieto, J. / Redondo, P. / Padro, D. / Blanco, F.J. / Paques, F. / Montoya, G.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage
Authors: Prieto, J. / Redondo, P. / Padro, D. / Arnould, S. / Epinat, J.C. / Paques, F. / Blanco, F.J. / Montoya, G.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI


Theoretical massNumber of molelcules
Total (without water)35,8692
Polymers35,8692
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.088, 69.088, 93.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DNA endonuclease I-CreI / LAGLIDAG HOMING ENDONUCLEASE / 23S rRNA intron protein


Mass: 17934.631 Da / Num. of mol.: 2 / Fragment: residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pet24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0960.25
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.97
SYNCHROTRONSLS X06SA21
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
211
ReflectionHighest resolution: 2 Å / Num. all: 25943 / Num. obs: 25943 / % possible obs: 93.2 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g9z

1g9z


Resolution: 2→34.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.652 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 1380 5.1 %RANDOM
Rwork0.18379 ---
obs0.18634 25943 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.251 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 262 2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222530
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9673416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44225116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41315484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0291512
X-RAY DIFFRACTIONr_chiral_restr0.1720.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021852
X-RAY DIFFRACTIONr_nbd_refined0.2320.21166
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_mcbond_it1.7851.51589
X-RAY DIFFRACTIONr_mcangle_it2.70222482
X-RAY DIFFRACTIONr_scbond_it4.09131099
X-RAY DIFFRACTIONr_scangle_it6.0494.5934
LS refinement shellResolution: 2.005→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 74 -
Rwork0.222 1289 -
obs--64.23 %

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