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- PDB-4aag: Crystal structure of the mutant D75N I-CreI in complex with its w... -

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Basic information

Entry
Database: PDB / ID: 4aag
TitleCrystal structure of the mutant D75N I-CreI in complex with its wild- type target in presence of Ca at the active site (The four central bases, 2NN region, are composed by GTAC from 5' to 3')
Components
  • 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3'
  • 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: 2.8 Å
AuthorsMolina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F. / Epinat, J.C. / Valton, J. / Grizot, S. / Duchateau, P. ...Molina, R. / Redondo, P. / Stella, S. / Marenchino, M. / D'Abramo, M. / Gervasio, F. / 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 / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3'
G: 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8486
Polymers49,7684
Non-polymers802
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-89.4 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.469, 71.413, 171.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 17515.137 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 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3'


Mass: 7368.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.9 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% PEG400, 0.1M HEPES PH 7.5, 0.1M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / 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: 2.8→47.47 Å / Num. obs: 15005 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 57.29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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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: 2.8→45.743 Å / SU ML: 0.77 / σ(F): 1.34 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1496 10.02 %
Rwork0.1735 --
obs0.1811 14934 99.48 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.086 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9561 Å20 Å20 Å2
2---17.5758 Å20 Å2
3---11.6197 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 978 2 40 3479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043599
X-RAY DIFFRACTIONf_angle_d0.9285067
X-RAY DIFFRACTIONf_dihedral_angle_d21.7431409
X-RAY DIFFRACTIONf_chiral_restr0.051578
X-RAY DIFFRACTIONf_plane_restr0.003476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.42481310.30871187X-RAY DIFFRACTION99
2.8904-2.99370.37231350.25411208X-RAY DIFFRACTION100
2.9937-3.11350.30671340.22691199X-RAY DIFFRACTION99
3.1135-3.25520.30981330.20261196X-RAY DIFFRACTION100
3.2552-3.42680.24321350.19491211X-RAY DIFFRACTION99
3.4268-3.64140.281320.18331191X-RAY DIFFRACTION100
3.6414-3.92240.23221360.17111223X-RAY DIFFRACTION99
3.9224-4.31680.24471360.13861221X-RAY DIFFRACTION99
4.3168-4.94090.1881360.12861216X-RAY DIFFRACTION99
4.9409-6.22250.24611400.15991253X-RAY DIFFRACTION100
6.2225-45.74950.21431480.16611333X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.1361 Å / Origin y: -27.0071 Å / Origin z: -23.6519 Å
111213212223313233
T0.1575 Å2-0.0592 Å20.0295 Å2-0.1399 Å2-0.0736 Å2--0.2169 Å2
L1.4844 °2-0.8421 °2-0.5835 °2-2.4013 °20.8116 °2--1.6044 °2
S0.0002 Å °0.0133 Å °0.0397 Å °0.1096 Å °-0.2193 Å °0.045 Å °0.0267 Å °-0.0777 Å °0.1759 Å °
Refinement TLS groupSelection details: ALL

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