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- PDB-5a72: Crystal structure of the homing endonuclease I-CvuI in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5a72
TitleCrystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Ca
Components
  • 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3'
  • DNA ENDONUCLEASE I-CVUI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds
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-CvuI
Similarity search - Component
Biological speciesCHLORELLA VULGARIS (plant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMolina, R. / Redondo, P. / LopezMendez, B. / Villate, M. / Merino, N. / Blanco, F.J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification
Authors: Molina, R. / Redondo, P. / Lopez-Mendez, B. / Villate, M. / Merino, N. / Blanco, F.J. / Valton, J. / Grizot, S. / Duchateau, P. / Prieto, J. / Montoya, G.
History
DepositionJul 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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-CVUI
B: DNA ENDONUCLEASE I-CVUI
C: 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3'
D: 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3776
Polymers53,2974
Non-polymers802
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-93.9 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.179, 94.210, 51.340
Angle α, β, γ (deg.)90.00, 104.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA ENDONUCLEASE I-CVUI / 23S RRNA INTRON PROTEIN / I-CVUI


Mass: 19278.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLORELLA VULGARIS (plant) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P56347, Hydrolases; Acting on ester bonds
#2: DNA chain 24MER DNA, 5'-D(*DTP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP *DCP*GP*AP*CP*GP*TP*TP*CP*TP*GP*A)-3'


Mass: 7369.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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: 2.39 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.6→47.1 Å / Num. obs: 14572 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 33.18 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9Y

1g9y


Resolution: 2.6→47.105 Å / SU ML: 0.33 / σ(F): 1.26 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 2722 9.9 %
Rwork0.1614 --
obs0.1685 14548 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 978 2 86 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083598
X-RAY DIFFRACTIONf_angle_d1.25060
X-RAY DIFFRACTIONf_dihedral_angle_d22.8991414
X-RAY DIFFRACTIONf_chiral_restr0.047599
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64730.40541460.29661238X-RAY DIFFRACTION92
2.6473-2.69820.32261490.26131369X-RAY DIFFRACTION97
2.6982-2.75330.31311460.25741265X-RAY DIFFRACTION97
2.7533-2.81320.30591340.22431292X-RAY DIFFRACTION95
2.8132-2.87860.28511440.23691322X-RAY DIFFRACTION98
2.8786-2.95060.29331460.23421310X-RAY DIFFRACTION98
2.9506-3.03030.28031460.21641329X-RAY DIFFRACTION97
3.0303-3.11950.2241380.19091243X-RAY DIFFRACTION94
3.1195-3.22010.29711470.17951354X-RAY DIFFRACTION97
3.2201-3.33520.29141400.16441269X-RAY DIFFRACTION95
3.3352-3.46870.28471450.1481343X-RAY DIFFRACTION98
3.4687-3.62650.221380.15411290X-RAY DIFFRACTION97
3.6265-3.81760.23331400.14191311X-RAY DIFFRACTION96
3.8176-4.05670.19371350.13081310X-RAY DIFFRACTION96
4.0567-4.36970.17951510.12341302X-RAY DIFFRACTION97
4.3697-4.80910.2151460.10951340X-RAY DIFFRACTION98
4.8091-5.5040.1591420.11651312X-RAY DIFFRACTION98
5.504-6.9310.18571410.14041334X-RAY DIFFRACTION98
6.931-47.11270.15811480.13571323X-RAY DIFFRACTION98

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