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- PDB-5a74: Crystal structure of the homing endonuclease I-CvuI in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5a74
TitleCrystal structure of the homing endonuclease I-CvuI in complex with its target (Sro1.3) in the presence of 2 mM Mn
Components
  • 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3'
  • 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-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: 2.5 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.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: 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'
D: 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'
E: 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3'
F: 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3999
Polymers53,2356
Non-polymers1653
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-91.4 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.730, 82.030, 94.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19292.533 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 14MER DNA, 5'-D(*TP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'


Mass: 4264.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 10MER DNA, 5'-D(*GP*AP*CP*GP*TP*TP*CP*TP*GP*AP)-3'


Mass: 3060.015 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.: 205 / 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: 2.43 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.8
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.5→62.63 Å / Num. obs: 17475 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 36.29 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % 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: 2.5→61.944 Å / SU ML: 0.26 / σ(F): 0.97 / Phase error: 33.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 3216 10.01 %
Rwork0.1862 --
obs0.1912 17305 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→61.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 980 3 205 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083600
X-RAY DIFFRACTIONf_angle_d1.235060
X-RAY DIFFRACTIONf_dihedral_angle_d21.6511410
X-RAY DIFFRACTIONf_chiral_restr0.072599
X-RAY DIFFRACTIONf_plane_restr0.004467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53730.32951370.28681263X-RAY DIFFRACTION99
2.5373-2.5770.33981370.2831254X-RAY DIFFRACTION99
2.577-2.61920.32131390.27751256X-RAY DIFFRACTION99
2.6192-2.66440.31931320.27481255X-RAY DIFFRACTION98
2.6644-2.71290.29341410.26491269X-RAY DIFFRACTION99
2.7129-2.7650.30741440.25971265X-RAY DIFFRACTION99
2.765-2.82150.31421350.25071254X-RAY DIFFRACTION98
2.8215-2.88280.31571420.25591257X-RAY DIFFRACTION99
2.8828-2.94990.32191430.2511285X-RAY DIFFRACTION100
2.9499-3.02370.27511380.23351253X-RAY DIFFRACTION99
3.0237-3.10540.24081440.21561260X-RAY DIFFRACTION99
3.1054-3.19680.28521370.19061245X-RAY DIFFRACTION99
3.1968-3.30.26161490.18211291X-RAY DIFFRACTION99
3.3-3.41790.20361460.16751249X-RAY DIFFRACTION99
3.4179-3.55470.18261390.17161268X-RAY DIFFRACTION99
3.5547-3.71650.21881390.1651254X-RAY DIFFRACTION99
3.7165-3.91240.17631410.15141290X-RAY DIFFRACTION99
3.9124-4.15750.21651430.15051242X-RAY DIFFRACTION99
4.1575-4.47840.20271450.14711268X-RAY DIFFRACTION100
4.4784-4.92890.1871380.13371270X-RAY DIFFRACTION99
4.9289-5.64170.18731460.16951257X-RAY DIFFRACTION99
5.6417-7.10630.21291390.17461267X-RAY DIFFRACTION99
7.1063-61.96310.20171220.14581129X-RAY DIFFRACTION88

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