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- PDB-3eh8: Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex w... -

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Basic information

Entry
Database: PDB / ID: 3eh8
TitleCrystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium
Components
  • (31-MER) x 2
  • Intron-encoded DNA endonuclease I-AniI
KeywordsHYDROLASE/DNA / Protein-DNA complex / Endonuclease / Hydrolase / Intron homing / Mitochondrion / mRNA processing / mRNA splicing / Nuclease / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


intron homing / RNA splicing / mRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. ...LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / : / Cytochrome b/b6/petB / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Intron-encoded DNA endonuclease I-AniI
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTakeuchi, R. / Stoddard, B.L.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.
Authors: Takeuchi, R. / Certo, M. / Caprara, M.G. / Scharenberg, A.M. / Stoddard, B.L.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intron-encoded DNA endonuclease I-AniI
D: Intron-encoded DNA endonuclease I-AniI
G: Intron-encoded DNA endonuclease I-AniI
B: 31-MER
C: 31-MER
E: 31-MER
F: 31-MER
H: 31-MER
I: 31-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,27715
Polymers146,0369
Non-polymers2406
Water1,20767
1
A: Intron-encoded DNA endonuclease I-AniI
B: 31-MER
C: 31-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7595
Polymers48,6793
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-57 kcal/mol
Surface area19630 Å2
MethodPISA
2
D: Intron-encoded DNA endonuclease I-AniI
E: 31-MER
F: 31-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7595
Polymers48,6793
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-63 kcal/mol
Surface area19500 Å2
MethodPISA
3
G: Intron-encoded DNA endonuclease I-AniI
H: 31-MER
I: 31-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7595
Polymers48,6793
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-56 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.555, 192.603, 161.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Intron-encoded DNA endonuclease I-AniI / mRNA maturase bI1 / COB intron protein / Truncated non-functional cytochrome b / DNA ...mRNA maturase bI1 / COB intron protein / Truncated non-functional cytochrome b / DNA endonuclease/RNA maturase I-AniI


Mass: 29611.490 Da / Num. of mol.: 3 / Fragment: Y2 I-AniI (UNP residues 237-488) / Mutation: F13Y, F80K, S111Y, L232K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: AnCOB Intron Gene / Plasmid: pET system / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL+
References: UniProt: P03880, Hydrolases; Acting on ester bonds
#2: DNA chain 31-MER


Mass: 9609.168 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: the physiological DNA target site of I-AniI in the mitochondrial apocytochrome B gene of A. nidulans
#3: DNA chain 31-MER


Mass: 9458.087 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: the physiological DNA target site of I-AniI in the mitochondrial apocytochrome B gene of A. nidulans
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 32% Polypropylene glycol P400, 0.08M Bis-Tris, 0.25M sodium chloride, 0.05M calucium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1Polypropylene glycol P40011
2Bis-Tris11
3sodium chloride11
4calucium chloride11
5Polypropylene glycol P40012
6Bis-Tris12
7sodium chloride12
8calucium chloride12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→37.14 Å / Num. all: 46294 / Num. obs: 44303 / % possible obs: 95.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.25 / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1P8K

1p8k


Resolution: 2.7→37.14 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 27.67 / SU ML: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25316 2126 5.1 %RANDOM
Rwork0.1978 ---
obs0.20057 39630 90.2 %-
all-43936 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 3795 6 67 10141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210650
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.42615162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76723.696276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.277151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0631536
X-RAY DIFFRACTIONr_chiral_restr0.0890.21698
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.24182
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26749
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2365
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.53904
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8926147
X-RAY DIFFRACTIONr_scbond_it0.96739064
X-RAY DIFFRACTIONr_scangle_it1.584.59015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 133 -
Rwork0.302 2504 -
obs--78.44 %
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)
10.82460.2866-0.4491.36470.05550.9187-0.00510.03420.06280.1052-0.027-0.0395-0.0026-0.04070.032-0.0507-0.0004-0.0436-0.04620.009-0.006928.7922-31.082-1.7586
24.3281.0013-2.53233.2793-0.88664.7885-0.1274-0.40880.11070.4705-0.0472-0.08460.21690.27110.1746-0.0689-0.0098-0.1289-0.19260.006-0.223532.3043-34.00527.2599
35.44070.271-0.12531.77420.4192.824-0.06620.3649-0.3336-0.1904-0.2047-0.19790.0895-0.08680.2709-0.18960.02980.0457-0.3440.0651-0.177414.7948-7.499528.9305
46.6781.49761.50052.92321.23894.1879-0.22531.0374-0.2422-0.5404-0.0505-0.204-0.3589-0.24370.2758-0.08690.07580.06810.00760.0625-0.182614.0698-3.293519.8707
51.91531.25940.00596.7874-0.25882.283-0.03580.21870.0325-0.3676-0.3223-0.5040.25280.29640.3582-0.34110.07210.0327-0.13210.1734-0.209739.7256-40.58455.54
60.3981-0.4563-0.29313.56120.80511.56-0.00630.1980.233-0.4945-0.1393-0.03750.17170.060.14560.01570.05620.0411-0.02850.0629-0.117135.9331-39.570745.9848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 254
2X-RAY DIFFRACTION2B1 - 31
3X-RAY DIFFRACTION2C1 - 31
4X-RAY DIFFRACTION3D1 - 254
5X-RAY DIFFRACTION4E1 - 31
6X-RAY DIFFRACTION4F1 - 31
7X-RAY DIFFRACTION5G1 - 254
8X-RAY DIFFRACTION6H1 - 31
9X-RAY DIFFRACTION6I1 - 31

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