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- PDB-4aqx: Crystal structure of I-CreI complexed with its target methylated ... -

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Basic information

Entry
Database: PDB / ID: 4aqx
TitleCrystal structure of I-CreI complexed with its target methylated at position plus 2 (in the b strand) in the presence of magnesium
Components
  • 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'
  • 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'
  • 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
  • 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3'
  • DNA ENDONUCLEASE I-CREI
KeywordsHYDROLASE / METHYLATION / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsValton, J. / Daboussi, F. / Leduc, S. / Redondo, P. / Macmaster, R. / Molina, R. / Montoya, G. / Duchateau, P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: 5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases.
Authors: Valton, J. / Daboussi, F. / Leduc, S. / Molina, R. / Redondo, P. / Macmaster, R. / Montoya, G. / Duchateau, P.
History
DepositionApr 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
C: 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3'
D: 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'
E: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'
F: 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,22814
Polymers49,6956
Non-polymers5338
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-98 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.839, 71.401, 179.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 17516.121 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-153
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 , 4 types, 4 molecules CDEF

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


Mass: 4288.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3'


Mass: 3100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3'


Mass: 4198.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3'


Mass: 3075.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 141 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.95 Å3/Da / Density % sol: 58.28 % / Description: NONE

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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 / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.79 Å / Num. obs: 30701 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 50.02 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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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 1G9Z

1g9z


Resolution: 2.2→45.793 Å / SU ML: 0.8 / σ(F): 1.34 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1998 6.5 %
Rwork0.2015 --
obs0.2041 30701 99.79 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.936 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.121 Å20 Å20 Å2
2---8.6003 Å20 Å2
3----3.5207 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 981 33 133 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013656
X-RAY DIFFRACTIONf_angle_d1.2795152
X-RAY DIFFRACTIONf_dihedral_angle_d23.121423
X-RAY DIFFRACTIONf_chiral_restr0.078578
X-RAY DIFFRACTIONf_plane_restr0.005476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.39681390.32712002X-RAY DIFFRACTION100
2.255-2.3160.33611400.29642015X-RAY DIFFRACTION100
2.316-2.38410.37841410.32072022X-RAY DIFFRACTION100
2.3841-2.46110.40171390.30792003X-RAY DIFFRACTION100
2.4611-2.54910.35691430.29262041X-RAY DIFFRACTION100
2.5491-2.65110.32821400.24752010X-RAY DIFFRACTION100
2.6511-2.77170.29921400.2522018X-RAY DIFFRACTION100
2.7717-2.91790.27631420.25082034X-RAY DIFFRACTION100
2.9179-3.10060.29121430.23522045X-RAY DIFFRACTION100
3.1006-3.340.23311410.19682046X-RAY DIFFRACTION100
3.34-3.67590.24711430.19662043X-RAY DIFFRACTION100
3.6759-4.20750.18311450.16872098X-RAY DIFFRACTION100
4.2075-5.29980.16671470.13762101X-RAY DIFFRACTION100
5.2998-45.80290.22671550.19032225X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.0581 Å / Origin y: 25.5431 Å / Origin z: -25.5515 Å
111213212223313233
T0.3051 Å2-0.033 Å2-0.0816 Å2-0.3003 Å20.0491 Å2--0.3224 Å2
L2.4134 °2-1.1993 °21.9738 °2-2.1327 °2-2.3737 °2--4.2129 °2
S-0.1945 Å °0.011 Å °0.1487 Å °0.3802 Å °-0.2611 Å °-0.1669 Å °-0.4079 Å °0.1685 Å °0.3596 Å °
Refinement TLS groupSelection details: ALL

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