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

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Basic information

Entry
Database: PDB / ID: 4aab
TitleCrystal structure of the mutant D75N I-CreI in complex with its wild- type target (The four central bases, 2NN region, are composed by GTAC from 5' to 3')
Components
  • 10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
  • 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-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
S-1,2-PROPANEDIOL / DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 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 / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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_auth_seq_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
D: 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'
E: 10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
F: 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'
G: 10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15415
Polymers49,6786
Non-polymers4769
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13760 Å2
ΔGint-83.1 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.970, 71.100, 46.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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

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DNA chain , 2 types, 4 molecules DFEG

#2: DNA chain 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'


Mass: 4248.793 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 10MER DNA 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'


Mass: 3075.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 131 molecules

#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.5 / Details: 30% PROPANEDIOL, 0.1M HEPES PH 7.5, 20% PEG400

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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: 2.5→44.51 Å / Num. obs: 20537 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 4.8 % / Biso Wilson estimate: 47.77 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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: 2.5→34.814 Å / SU ML: 0.84 / σ(F): 0 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1079 5.2 %
Rwork0.17 --
obs0.1728 20609 99.68 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.862 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3022 Å20 Å20 Å2
2--1.8321 Å20 Å2
3----1.5298 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 980 29 122 3603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143654
X-RAY DIFFRACTIONf_angle_d1.2725152
X-RAY DIFFRACTIONf_dihedral_angle_d22.131418
X-RAY DIFFRACTIONf_chiral_restr0.065585
X-RAY DIFFRACTIONf_plane_restr0.004476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61380.36641260.27332415X-RAY DIFFRACTION100
2.6138-2.75160.25711480.22522390X-RAY DIFFRACTION100
2.7516-2.92390.30071140.1922406X-RAY DIFFRACTION100
2.9239-3.14950.27611490.18022400X-RAY DIFFRACTION100
3.1495-3.46620.17161220.14672412X-RAY DIFFRACTION100
3.4662-3.96710.21451500.15522442X-RAY DIFFRACTION100
3.9671-4.99580.18371340.14352469X-RAY DIFFRACTION100
4.9958-34.81730.23031360.17882596X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 23.9366 Å / Origin y: 26.9491 Å / Origin z: 11.3878 Å
111213212223313233
T0.2082 Å2-0.0271 Å20.014 Å2-0.2849 Å2-0.0819 Å2--0.1974 Å2
L2.1595 °21.8733 °2-1.1308 °2-4.2962 °2-2.0052 °2--2.2844 °2
S0.1627 Å °-0.0889 Å °0.0268 Å °0.0627 Å °-0.169 Å °0.0777 Å °0.0651 Å °-0.0192 Å °-0.0004 Å °
Refinement TLS groupSelection details: ALL

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