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- PDB-6fb1: Crystal Structure of a Tailored I-CreI Homing Endonuclease Protei... -

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Basic information

Entry
Database: PDB / ID: 6fb1
TitleCrystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with its target DNA (Haemoglobin beta subunit gene) in the presence of Magnesium
Components
  • (DNA endonuclease I- ...) x 2
  • DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*CP*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*GP*AP*AP*GP*TP*CP*TP*GP*A)-3')
  • DNA (5'-D(P*AP*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 / 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: 3.024 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*GP*AP*CP*TP*TP*CP*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*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')
G: DNA (5'-D(P*AP*GP*AP*AP*GP*TP*CP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9479
Polymers49,8746
Non-polymers733
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-95 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.090, 66.600, 91.780
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA endonuclease I- ... , 2 types, 2 molecules AB

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


Mass: 17641.312 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, Hydrolases; Acting on ester bonds
#2: Protein DNA endonuclease I-CreI / 23S rRNA intron protein


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, Hydrolases; Acting on ester bonds

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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*CP*TP*CP*CP*AP*C)-3')


Mass: 4175.730 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*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')


Mass: 3118.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*AP*GP*AP*AP*GP*TP*CP*TP*GP*A)-3')


Mass: 3093.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 18 molecules

#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 / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate 0.1 M sodium acetate pH 4.6 35% (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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→66.6 Å / Num. obs: 18027 / % possible obs: 99.7 % / Redundancy: 2.4 % / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.15 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: 3.024→33.985 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 35.32
RfactorNum. reflection% reflection
Rfree0.2518 906 5.03 %
Rwork0.2081 --
obs0.2103 18027 86.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.024→33.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 980 3 15 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023631
X-RAY DIFFRACTIONf_angle_d0.6965111
X-RAY DIFFRACTIONf_dihedral_angle_d20.9121421
X-RAY DIFFRACTIONf_chiral_restr0.04584
X-RAY DIFFRACTIONf_plane_restr0.003476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0239-3.21320.36061040.33471873X-RAY DIFFRACTION57
3.2132-3.4610.33311580.27923048X-RAY DIFFRACTION93
3.461-3.80890.35431600.2612960X-RAY DIFFRACTION91
3.8089-4.35910.30021620.23073100X-RAY DIFFRACTION94
4.3591-5.48830.22121640.18733079X-RAY DIFFRACTION94
5.4883-33.98720.20141580.16923061X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 6.2003 Å / Origin y: -14.4856 Å / Origin z: 113.9935 Å
111213212223313233
T0.1314 Å20.013 Å2-0.03 Å2-0.364 Å2-0.0097 Å2--0.213 Å2
L1.0757 °20.0242 °2-0.1961 °2-2.7741 °20.609 °2--3.0531 °2
S0.1141 Å °0.0249 Å °0.004 Å °0.2795 Å °-0.4798 Å °0.2234 Å °-0.1576 Å °-0.7567 Å °0.2094 Å °
Refinement TLS groupSelection details: all

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