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- PDB-6fb9: Crystal Structure of the I-CreI Homing Endonuclease D75N variant ... -

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Basic information

Entry
Database: PDB / ID: 6fb9
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 Manganese
Components
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*CP*AP*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 / 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: 2.95 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
E: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
C: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*TP*GP*CP*GP*TP*AP*C)-3')
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
F: DNA (5'-D(P*GP*CP*AP*GP*TP*TP*TP*TP*GP*A)-3')
D: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,54115
Polymers49,9626
Non-polymers5799
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13440 Å2
ΔGint-79 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.729, 79.729, 126.250
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 , 4 types, 4 molecules ECFD

#1: 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.: 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*C)-3')


Mass: 4248.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*AP*GP*TP*TP*TP*TP*GP*A)-3')


Mass: 3075.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')


Mass: 3075.026 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, 31 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#8: 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: 4.02 Å3/Da / Density % sol: 69.41 %
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: 1.8 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: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.95→49.49 Å / Num. obs: 32279 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9Z

1g9z


Resolution: 2.95→42.049 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2033 3248 10.06 %
Rwork0.1676 --
obs0.1712 32279 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→42.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 980 25 22 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013645
X-RAY DIFFRACTIONf_angle_d1.2945123
X-RAY DIFFRACTIONf_dihedral_angle_d22.7991421
X-RAY DIFFRACTIONf_chiral_restr0.05587
X-RAY DIFFRACTIONf_plane_restr0.006479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.99410.36651380.32111242X-RAY DIFFRACTION98
2.9941-3.04080.3311420.29851279X-RAY DIFFRACTION97
3.0408-3.09070.31891300.27181229X-RAY DIFFRACTION98
3.0907-3.14390.3131400.26731254X-RAY DIFFRACTION97
3.1439-3.20110.29931380.23671243X-RAY DIFFRACTION98
3.2011-3.26260.35761460.21881260X-RAY DIFFRACTION98
3.2626-3.32920.21651520.19641270X-RAY DIFFRACTION98
3.3292-3.40160.22661400.17631230X-RAY DIFFRACTION98
3.4016-3.48070.22681360.18361275X-RAY DIFFRACTION99
3.4807-3.56770.21481480.19111237X-RAY DIFFRACTION99
3.5677-3.66410.26131380.18131263X-RAY DIFFRACTION99
3.6641-3.77180.21271360.18051307X-RAY DIFFRACTION99
3.7718-3.89350.24191420.16781223X-RAY DIFFRACTION99
3.8935-4.03250.20751480.16751302X-RAY DIFFRACTION99
4.0325-4.19380.20641400.15231240X-RAY DIFFRACTION97
4.1938-4.38450.14721420.13631238X-RAY DIFFRACTION99
4.3845-4.61540.151380.13291277X-RAY DIFFRACTION99
4.6154-4.90420.17241360.12921292X-RAY DIFFRACTION99
4.9042-5.28220.14851400.13791262X-RAY DIFFRACTION99
5.2822-5.81250.16421410.13791282X-RAY DIFFRACTION100
5.8125-6.65070.17591380.14621298X-RAY DIFFRACTION100
6.6507-8.36840.20111520.14691254X-RAY DIFFRACTION100
8.3684-42.05280.15171470.15571274X-RAY DIFFRACTION99

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