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- PDB-3oor: I-SceI mutant (K86R/G100T)complexed with C/G+4 DNA substrate -

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Basic information

Entry
Database: PDB / ID: 3oor
TitleI-SceI mutant (K86R/G100T)complexed with C/G+4 DNA substrate
Components
  • 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3'
  • 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3'
  • Intron encoded endonuclease I-SceI
KeywordsHYDROLASE/DNA / homing endonuclease / intron homing / LAGLIDADG / Hydrolase-DNA complex / I-SceI mutant (K86R/G100T)
Function / homology
Function and homology information


Group II intron splicing / intron homing / mRNA cis splicing, via spliceosome / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
LAGLIDADG DNA endonuclease family / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Intron-encoded endonuclease I-SceI
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJoshi, R. / Chen, J.-H. / Golden, B.L. / Gimble, F.S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity.
Authors: Joshi, R. / Ho, K.K. / Tenney, K. / Chen, J.H. / Golden, B.L. / Gimble, F.S.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 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.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_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: Intron encoded endonuclease I-SceI
C: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3'
D: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5376
Polymers43,4173
Non-polymers1203
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-81 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.701, 50.538, 62.931
Angle α, β, γ (deg.)90.000, 108.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Intron encoded endonuclease I-SceI / 21S rRNA intron maturase / Homing endonuclease omega


Mass: 28058.629 Da / Num. of mol.: 1 / Mutation: K86R, G100T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SceI,omega / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03882, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*AP*AP*TP*AP*C)-3'


Mass: 7717.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Top strand of I-SceI C/G+4 DNA target
#3: DNA chain 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*CP*CP*CP*TP*AP*GP*CP*GP*T)-3'


Mass: 7640.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bottom strand of I-SceI C/G+4 DNA target
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: PEG400,CaCl2,NaOAc,DTT, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13729 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.057 / Χ2: 1.806 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.547.20.4016711.79398.8
2.54-2.597.60.3786882.04699.4
2.59-2.647.60.3486862.18599.4
2.64-2.697.60.2886762.06799.7
2.69-2.757.60.2526802.32499.3
2.75-2.827.70.2096851.88899.7
2.82-2.897.60.1676701.85799.6
2.89-2.967.70.1396831.82699.6
2.96-3.057.60.1266861.7599.9
3.05-3.157.60.0916991.67199.6
3.15-3.267.50.0776651.64299.7
3.26-3.397.40.0616841.74199.7
3.39-3.557.30.0616871.90599.9
3.55-3.737.30.0616861.99999.9
3.73-3.976.40.0547001.87599.6
3.97-4.277.30.0486831.58899.7
4.27-4.77.20.0457011.634100
4.7-5.387.20.0437001.537100
5.38-6.787.20.046981.42999.9
6.78-506.50.0367011.25595.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R7M

1r7m


Resolution: 2.5→31.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 32.849 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 1033 7.6 %RANDOM
Rwork0.2347 ---
all0.32 13795 --
obs0.2382 13630 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 156.52 Å2 / Biso mean: 68.3147 Å2 / Biso min: 12.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å2-0.12 Å2
2--0.12 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 984 3 11 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223008
X-RAY DIFFRACTIONr_angle_refined_deg1.0112.3684273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3435222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90625.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40515356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.055155
X-RAY DIFFRACTIONr_chiral_restr0.0550.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211929
X-RAY DIFFRACTIONr_mcbond_it0.1811.51114
X-RAY DIFFRACTIONr_mcangle_it0.33621811
X-RAY DIFFRACTIONr_scbond_it0.35531894
X-RAY DIFFRACTIONr_scangle_it0.5984.52462
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 82 -
Rwork0.396 898 -
all-980 -
obs--98 %
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)
14.9111-2.2913-3.88686.23455.074410.0469-0.0346-0.0073-0.13130.3735-0.15090.08330.0288-0.51510.18550.08890.1018-0.0640.2205-0.06270.2367-25.965617.330213.8379
23.9834-1.0871-2.19965.10534.69318.46050.00490.0961-0.06210.4148-0.43630.3271-0.1059-0.78760.43140.19530.1142-0.12910.2712-0.09260.3108-25.511915.696613.953
33.7161-0.3963-1.00123.39221.74216.02810.29870.14070.2006-0.2712-0.0479-0.2762-1.0138-0.074-0.25090.27520.0973-0.07730.23320.01950.3105-16.658725.15358.0614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 25
2X-RAY DIFFRACTION2D2 - 25
3X-RAY DIFFRACTION3A3 - 225

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