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- PDB-3c0x: I-SceI in complex with a top nicked DNA substrate -

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Basic information

Entry
Database: PDB / ID: 3c0x
TitleI-SceI in complex with a top nicked DNA substrate
Components
  • DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3')
  • DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3')
  • DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3')
  • Intron-encoded endonuclease I-SceI
Keywordshydrolase/DNA / endonuclease / homing / LADLIDADG / catalytic mechanism / metal binding / nicked intermediate / Hydrolase / Intron homing / Mitochondrion / mRNA processing / mRNA splicing / hydrolase-DNA COMPLEX
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: 2.3 Å
AuthorsMoure, C.M. / Gimble, F.S. / Quiocho, F.A.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
Authors: Moure, C.M. / Gimble, F.S. / Quiocho, F.A.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_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_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
B: DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3')
C: DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3')
D: DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3')
A: Intron-encoded endonuclease I-SceI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1497
Polymers43,0294
Non-polymers1203
Water1,04558
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.680, 80.680, 128.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3')


Mass: 4313.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA SYNTHETIC PRODUCT
#2: DNA chain DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3')


Mass: 3382.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA SYNTHETIC PRODUCT
#3: DNA chain DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3')


Mass: 7615.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA SYNTHETIC PRODUCT

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Protein , 1 types, 1 molecules A

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


Mass: 27717.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCEI, OMEGA, SECY / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P03882, Hydrolases; Acting on ester bonds

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Non-polymers , 2 types, 61 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsHETATOM RENUMBERING CA 1-3 IN PUBLICATION CORRESPONDS TO CA 301-303 IN THE PDB FILE. HOH 1-58 IN ...HETATOM RENUMBERING CA 1-3 IN PUBLICATION CORRESPONDS TO CA 301-303 IN THE PDB FILE. HOH 1-58 IN PUBLICATION CORRESPONDS TO HOH 401-458 IN THE PDB FILE. THE PUTATIVE NUCLEOPHILIC WATER 28 IN PUBLICATION CORRESPONDS TO HOH A428 IN THE PDB FILE.

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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: 49.31 %
Crystal growTemperature: 277 K / pH: 4.6
Details: 22-26% 2-methyl-2,4-pentanediol (MPD) (v/v), 20 mM CaCl2, 1 mM dithiothreitol, 100 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.60
Components of the solutions
IDNameCrystal-IDSol-ID
1dithiothreitol11
2CaCl211
32-methyl-2,4-pentanediol12
4CaCl212
5dithiothreitol12
6sodium acetate12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19007 / % possible obs: 99.7 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R7M

1r7m


Resolution: 2.3→36.08 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.288 922 -
Rwork0.255 --
obs0.255 18872 96.8 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.437 Å23.437 Å2-6.873 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 979 3 58 2901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.34 Å /
RfactorNum. reflection
Rfree0.399 53
Rwork0.352 -

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