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- PDB-4aae: Crystal structure of the mutant D75N I-CreI in complex with an al... -

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Basic information

Entry
Database: PDB / ID: 4aae
TitleCrystal structure of the mutant D75N I-CreI in complex with an altered target (The four central bases, 2NN region, are composed by AGCG from 5' to 3')
Components
  • (24MER DNA) x 2
  • DNA ENDONUCLEASE I-CREI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMolina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Epinat, J.C. / Valton, J. / Grizot, S. / Duchateau, P. ...Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Epinat, J.C. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage.
Authors: Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Charles Epinat, J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G.
History
DepositionDec 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Data collection / Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _citation.page_last / _database_2.pdbx_DOI ..._citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ENDONUCLEASE I-CREI
B: DNA ENDONUCLEASE I-CREI
E: 24MER DNA
G: 24MER DNA


Theoretical massNumber of molelcules
Total (without water)49,9434
Polymers49,9434
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-51.8 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.150, 70.340, 172.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11G-2001-

HOH

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Components

#1: Protein DNA ENDONUCLEASE I-CREI / I-CREI / 23S RRNA INTRON PROTEIN


Mass: 17602.215 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#2: DNA chain 24MER DNA


Mass: 7393.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 24MER DNA


Mass: 7344.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 75 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 75 TO ASN

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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: 2.98 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 9.5 / Details: 50% PEG400, 0.1M CHES PH 9.5, 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→65.12 Å / Num. obs: 18671 / % possible obs: 97.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 33.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE0

2xe0


Resolution: 2.6→54.485 Å / SU ML: 0.67 / σ(F): 1.36 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1863 10 %
Rwork0.1752 --
obs0.1819 18626 97.46 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.884 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.7623 Å20 Å20 Å2
2---12.4378 Å20 Å2
3---3.6754 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 978 0 150 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073620
X-RAY DIFFRACTIONf_angle_d1.2625096
X-RAY DIFFRACTIONf_dihedral_angle_d22.9611426
X-RAY DIFFRACTIONf_chiral_restr0.068581
X-RAY DIFFRACTIONf_plane_restr0.004477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.67050.30451400.22981261X-RAY DIFFRACTION98
2.6705-2.7490.33331430.23471288X-RAY DIFFRACTION98
2.749-2.83780.32481380.22461241X-RAY DIFFRACTION97
2.8378-2.93920.27471430.20071288X-RAY DIFFRACTION99
2.9392-3.05680.30851430.20191287X-RAY DIFFRACTION98
3.0568-3.1960.2751420.18791274X-RAY DIFFRACTION98
3.196-3.36440.24821400.17941255X-RAY DIFFRACTION97
3.3644-3.57520.24871450.16541314X-RAY DIFFRACTION99
3.5752-3.85120.24961450.16951302X-RAY DIFFRACTION99
3.8512-4.23860.21471440.14391305X-RAY DIFFRACTION99
4.2386-4.85160.19041460.13541305X-RAY DIFFRACTION97
4.8516-6.11120.21191470.15771329X-RAY DIFFRACTION97
6.1112-54.49740.20061470.18911314X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -12.0278 Å / Origin y: -8.6733 Å / Origin z: 23.8832 Å
111213212223313233
T0.1276 Å20.0126 Å2-0.0307 Å2-0.2844 Å2-0.0819 Å2--0.1917 Å2
L0.6506 °20.495 °20.3136 °2-1.7058 °20.639 °2--0.8591 °2
S0.015 Å °-0.0007 Å °-0.0083 Å °-0.0386 Å °-0.1837 Å °0.0448 Å °-0.0218 Å °-0.001 Å °0.1479 Å °
Refinement TLS groupSelection details: ALL

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