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- PDB-6fb7: Crystal Structure of the I-CreI Homing Endonuclease D75N variant ... -

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Basic information

Entry
Database: PDB / ID: 6fb7
TitleCrystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with its target DNA in the presence of Manganese
Components
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*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
: / DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.689 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
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
D: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
E: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
F: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
G: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8439
Polymers49,6786
Non-polymers1653
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-86 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.504, 169.153, 49.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 17515.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: synthetic construct (others)
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')


Mass: 4248.793 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')


Mass: 3075.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
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: 1.6 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.689→49.02 Å / Num. obs: 30910 / % possible obs: 97.1 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.1
Reflection shellResolution: 2.69→2.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9Z

1g9z


Resolution: 2.689→49.015 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2114 3097 10.02 %
Rwork0.163 --
obs0.1677 30910 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.689→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 980 3 22 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093630
X-RAY DIFFRACTIONf_angle_d0.9925121
X-RAY DIFFRACTIONf_dihedral_angle_d21.2621418
X-RAY DIFFRACTIONf_chiral_restr0.053580
X-RAY DIFFRACTIONf_plane_restr0.004476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6889-2.73090.40071100.3243993X-RAY DIFFRACTION75
2.7309-2.77560.34651460.26151289X-RAY DIFFRACTION100
2.7756-2.82350.33611420.2481294X-RAY DIFFRACTION99
2.8235-2.87480.29611500.22611335X-RAY DIFFRACTION100
2.8748-2.93010.29121340.20571265X-RAY DIFFRACTION100
2.9301-2.98990.24611520.22111325X-RAY DIFFRACTION100
2.9899-3.05490.24511440.21731312X-RAY DIFFRACTION100
3.0549-3.1260.25251480.21471267X-RAY DIFFRACTION100
3.126-3.20410.28841480.18471324X-RAY DIFFRACTION100
3.2041-3.29080.21841490.1681296X-RAY DIFFRACTION100
3.2908-3.38760.23161450.1521276X-RAY DIFFRACTION100
3.3876-3.49690.21761510.15661337X-RAY DIFFRACTION100
3.4969-3.62180.20551400.16941287X-RAY DIFFRACTION100
3.6218-3.76680.2295820.1664776X-RAY DIFFRACTION58
3.7668-3.93820.18341370.1511293X-RAY DIFFRACTION100
3.9382-4.14570.18731500.14411308X-RAY DIFFRACTION100
4.1457-4.40530.19911410.12641308X-RAY DIFFRACTION100
4.4053-4.74510.13311440.12661305X-RAY DIFFRACTION100
4.7451-5.22220.19671420.13031302X-RAY DIFFRACTION100
5.2222-5.97670.17621480.14091310X-RAY DIFFRACTION100
5.9767-7.52560.21421430.14841292X-RAY DIFFRACTION100
7.5256-49.02310.15431510.15151319X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.4782 Å / Origin y: 192.7005 Å / Origin z: 12.5499 Å
111213212223313233
T0.2928 Å20.0828 Å20.0615 Å2-0.3267 Å20.0443 Å2--0.2415 Å2
L1.8625 °2-1.3057 °21.0541 °2-1.9562 °2-0.9718 °2--2.0652 °2
S-0.2495 Å °-0.1801 Å °-0.1225 Å °0.2191 Å °0.2541 Å °0.1785 Å °-0.0469 Å °0.03 Å °0.0136 Å °
Refinement TLS groupSelection details: all

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