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- PDB-6fb8: Crystal Structure of the I-CreI Homing Endonuclease D75N variant ... -

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Basic information

Entry
Database: PDB / ID: 6fb8
TitleCrystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with an altered version of its target DNA at 5NNN region in the presence of Magnesium
Components
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP*GP*CP*AP*GP*TP*TP*TP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
  • DNA endonuclease I-CreI
KeywordsDNA BINDING PROTEIN / Chlamydomonas reinhardtii
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
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: 2.45 Å
AuthorsMolina, R. / Prieto, J.
CitationJournal: Sci Rep / Year: 2018
Title: Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Authors: Prieto, J. / Redondo, P. / Lopez-Mendez, B. / D'Abramo, M. / Merino, N. / Blanco, F.J. / Duchateau, P. / Montoya, G. / Molina, R.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP*GP*CP*AP*GP*TP*TP*TP*TP*GP*A)-3')
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,45412
Polymers50,0524
Non-polymers4028
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-78 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.480, 79.480, 125.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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DNA chain , 2 types, 2 molecules DC

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


Mass: 7368.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')


Mass: 7368.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#3: Protein DNA endonuclease I-CreI / 23S rRNA intron protein


Mass: 17657.293 Da / Num. of mol.: 2
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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Non-polymers , 3 types, 94 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→27.44 Å / Num. obs: 56079 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.4
Reflection shellResolution: 2.45→2.58 Å / Rmerge(I) obs: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9Y

1g9y


Resolution: 2.45→27.424 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.2235 3884 6.93 %
Rwork0.1863 --
obs0.1889 56079 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→27.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 978 24 87 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013654
X-RAY DIFFRACTIONf_angle_d1.2275138
X-RAY DIFFRACTIONf_dihedral_angle_d22.5511434
X-RAY DIFFRACTIONf_chiral_restr0.045588
X-RAY DIFFRACTIONf_plane_restr0.006481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.480.39911500.31271914X-RAY DIFFRACTION99
2.48-2.51130.29171350.30051844X-RAY DIFFRACTION99
2.5113-2.54440.30781420.28241882X-RAY DIFFRACTION100
2.5444-2.57920.35671340.28381829X-RAY DIFFRACTION100
2.5792-2.6160.37081400.26931896X-RAY DIFFRACTION100
2.616-2.6550.33351420.26141934X-RAY DIFFRACTION100
2.655-2.69650.32111320.26181795X-RAY DIFFRACTION100
2.6965-2.74060.341350.29841922X-RAY DIFFRACTION99
2.7406-2.78790.38071240.29061787X-RAY DIFFRACTION98
2.7879-2.83850.35361520.26841914X-RAY DIFFRACTION99
2.8385-2.8930.30611330.26391819X-RAY DIFFRACTION99
2.893-2.9520.21361390.23911861X-RAY DIFFRACTION99
2.952-3.01610.25891350.22641876X-RAY DIFFRACTION99
3.0161-3.08620.30941410.23391852X-RAY DIFFRACTION100
3.0862-3.16330.26451440.23511908X-RAY DIFFRACTION100
3.1633-3.24870.23111360.21471831X-RAY DIFFRACTION100
3.2487-3.34410.20651440.18541874X-RAY DIFFRACTION100
3.3441-3.45180.26331420.19331905X-RAY DIFFRACTION100
3.4518-3.5750.24151370.19861845X-RAY DIFFRACTION100
3.575-3.71780.25551420.19221882X-RAY DIFFRACTION100
3.7178-3.88650.24411400.18331864X-RAY DIFFRACTION99
3.8865-4.09080.20651280.16921780X-RAY DIFFRACTION96
4.0908-4.34620.20871470.16151873X-RAY DIFFRACTION99
4.3462-4.68020.19071390.14611900X-RAY DIFFRACTION99
4.6802-5.14840.18391330.15721828X-RAY DIFFRACTION100
5.1484-5.8870.21211380.1471889X-RAY DIFFRACTION100
5.887-7.39280.16391410.15581833X-RAY DIFFRACTION98
7.3928-27.42580.12291390.12771858X-RAY DIFFRACTION99

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