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- PDB-6fb6: Crystal Structure of a Tailored I-CreI Homing Endonuclease Protei... -

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Basic information

Entry
Database: PDB / ID: 6fb6
TitleCrystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Manganese
Components
  • (I-CreI monomer ...) x 2
  • DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*C)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*G)-3')
  • DNA (5'-D(P*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')
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
: / DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: I-CreI monomer A
B: I-CreI monomer B
D: DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*C)-3')
F: DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*G)-3')
E: DNA (5'-D(P*GP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')
G: DNA (5'-D(P*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9429
Polymers49,7776
Non-polymers1653
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-91 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.176, 67.987, 83.044
Angle α, β, γ (deg.)90.00, 96.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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I-CreI monomer ... , 2 types, 2 molecules AB

#1: Protein I-CreI monomer A


Mass: 17528.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS
#2: Protein I-CreI monomer B


Mass: 17583.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS

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DNA chain , 4 types, 4 molecules DFEG

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


Mass: 4215.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*G)-3')


Mass: 4262.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*GP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')


Mass: 3134.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')


Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 14 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
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 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.6→44.89 Å / Num. obs: 28700 / % possible obs: 96.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.54

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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: 2.6→44.89 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.2422 2881 10.04 %
Rwork0.1929 --
obs0.1978 28700 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 981 3 11 3472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033620
X-RAY DIFFRACTIONf_angle_d0.785094
X-RAY DIFFRACTIONf_dihedral_angle_d21.1091416
X-RAY DIFFRACTIONf_chiral_restr0.046583
X-RAY DIFFRACTIONf_plane_restr0.003474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64260.33161360.29211231X-RAY DIFFRACTION94
2.6426-2.68820.27631400.27721257X-RAY DIFFRACTION97
2.6882-2.73710.3271350.27121212X-RAY DIFFRACTION97
2.7371-2.78970.3751350.27341216X-RAY DIFFRACTION94
2.7897-2.84670.33791400.26731254X-RAY DIFFRACTION96
2.8467-2.90850.27581410.24741280X-RAY DIFFRACTION98
2.9085-2.97620.32951350.24341236X-RAY DIFFRACTION95
2.9762-3.05060.32811370.23491246X-RAY DIFFRACTION97
3.0506-3.13310.27381420.24221254X-RAY DIFFRACTION98
3.1331-3.22520.30851380.21631250X-RAY DIFFRACTION94
3.2252-3.32930.23851390.18461251X-RAY DIFFRACTION98
3.3293-3.44820.22791360.1851221X-RAY DIFFRACTION94
3.4482-3.58630.23141380.18591248X-RAY DIFFRACTION98
3.5863-3.74940.2678920.1876775X-RAY DIFFRACTION59
3.7494-3.9470.21861390.19361238X-RAY DIFFRACTION99
3.947-4.19410.24171450.1651278X-RAY DIFFRACTION97
4.1941-4.51760.19391440.16771276X-RAY DIFFRACTION98
4.5176-4.97170.21731440.15131285X-RAY DIFFRACTION100
4.9717-5.68990.17171410.17541268X-RAY DIFFRACTION98
5.6899-7.1640.25031410.18871272X-RAY DIFFRACTION99
7.164-44.89640.18861430.15231271X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 38.3742 Å / Origin y: 12.482 Å / Origin z: 185.1541 Å
111213212223313233
T0.1459 Å2-0.0042 Å20.0256 Å2-0.192 Å20.0272 Å2--0.1788 Å2
L2.4541 °2-0.2192 °20.5956 °2-0.4852 °2-0.2831 °2--1.6186 °2
S-0.0133 Å °0.0104 Å °0.1433 Å °0.035 Å °-0.1794 Å °0.0432 Å °0.0197 Å °0.1221 Å °0.1533 Å °
Refinement TLS groupSelection details: all

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