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- PDB-3qqy: Crystal structure of a novel LAGLIDADG homing endonuclease, I-Onu... -

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Basic information

Entry
Database: PDB / ID: 3qqy
TitleCrystal structure of a novel LAGLIDADG homing endonuclease, I-OnuI (from Ophiostoma novo-ulmi subsp. americana)
Components
  • (DNA (26-MER)) x 2
  • Ribosomal protein 3/homing endonuclease-like protein fusion
KeywordsHYDROLASE/DNA / Protein-DNA comlex / LAGLIDADG family / Hydrolase / DNA binding / Mitochondrion / HYDROLASE-DNA complex
Function / homology
Function and homology information


endonuclease activity / ribosome / mitochondrion / 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) / Ribosomal protein 3/homing endonuclease-like protein fusion
Similarity search - Component
Biological speciesOphiostoma novo-ulmi subsp. americana (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsTakeuchi, R. / Stoddard, B.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Tapping natural reservoirs of homing endonucleases for targeted gene modification.
Authors: Takeuchi, R. / Lambert, A.R. / Mak, A.N. / Jacoby, K. / Dickson, R.J. / Gloor, G.B. / Scharenberg, A.M. / Edgell, D.R. / Stoddard, B.L.
History
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _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: Ribosomal protein 3/homing endonuclease-like protein fusion
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1724
Polymers51,1473
Non-polymers241
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-62 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.948, 73.933, 166.930
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 Ribosomal protein 3/homing endonuclease-like protein fusion


Mass: 35174.859 Da / Num. of mol.: 1 / Fragment: UNP Residues 413-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiostoma novo-ulmi subsp. americana (fungus)
Gene: rps3/HEG fusion / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q4VWW5
#2: DNA chain DNA (26-MER)


Mass: 7759.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Target sequence for the co-crystallized protein
#3: DNA chain DNA (26-MER)


Mass: 8213.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Target sequence for the co-crystallized protein
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 100 mM ammonium sulfate, 25% PEG 300, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 19182 / Num. obs: 18568 / % possible obs: 96.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.62 / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P8K

1p8k


Resolution: 2.401→44.46 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 16.343 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 955 5.2 %RANDOM
Rwork0.18887 ---
obs0.19145 17525 96.54 %-
all-18153 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0 Å20 Å2
2---3.29 Å2-0 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.401→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 1060 1 73 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223652
X-RAY DIFFRACTIONr_angle_refined_deg2.2172.3295140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06825.37108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96415490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.518157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022324
X-RAY DIFFRACTIONr_mcbond_it0.8671.51481
X-RAY DIFFRACTIONr_mcangle_it1.62522399
X-RAY DIFFRACTIONr_scbond_it2.51132171
X-RAY DIFFRACTIONr_scangle_it3.5854.52741
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 68 -
Rwork0.227 1172 -
obs-1172 90.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6583-0.3184-0.51250.98530.8943.03470.04810.04880.0688-0.0536-0.02770.0002-0.0433-0.063-0.02040.0716-0.00490.03820.00760.0230.2168-7.31483.036936.0521
20.4819-0.03680.63320.63630.73535.72430.14820.0302-0.01220.00830.0880.01640.3732-0.226-0.23620.15230.00960.03740.06990.01540.2148-12.0311-5.630934.6087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 303
2X-RAY DIFFRACTION2B1 - 26
3X-RAY DIFFRACTION2C1 - 26

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