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- PDB-1i3j: CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEAS... -

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Basic information

Entry
Database: PDB / ID: 1i3j
TitleCRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF INTRON ENDONUCLEASE I-TEVI WITH ITS SUBSTRATE
Components
  • 5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*A)-3'
  • 5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3'
  • INTRON-ASSOCIATED ENDONUCLEASE 1
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / EXTENDED STRUCTURE / ZN-FINGER / MINOR GROOVE HELIX / HELIX-TURN-HELIX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


double-stranded DNA endonuclease activity / nucleic acid metabolic process / intron homing / DNA-binding transcription repressor activity / transcription repressor complex / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
NUMOD3 motif / Nuclease associated modular domain 3 / Intron endonuclease, group I / : / Intron-encoded endonuclease 1, DNA-binding domain / Intron-encoded nuclease repeat 2 / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Intron-associated endonuclease 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsVan Roey, P. / Waddling, C.A. / Fox, K.M. / Belfort, M. / Derbyshire, V.
CitationJournal: EMBO J. / Year: 2001
Title: Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.
Authors: Van Roey, P. / Waddling, C.A. / Fox, K.M. / Belfort, M. / Derbyshire, V.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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: 5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3'
C: 5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*A)-3'
A: INTRON-ASSOCIATED ENDONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1914
Polymers26,1263
Non-polymers651
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.140, 65.210, 43.670
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*TP*TP*CP*TP*TP*GP*GP*GP*TP*CP*TP*AP*CP*CP*GP*TP*TP*TP*AP*AP*T)-3'


Mass: 6410.141 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*TP*TP*AP*AP*AP*CP*GP*GP*TP*AP*GP*AP*CP*CP*CP*AP*AP*GP*A)-3'


Mass: 6473.239 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein INTRON-ASSOCIATED ENDONUCLEASE 1 / I-TEVI


Mass: 13242.219 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid: PET-3A / Production host: Escherichia coli (E. coli)
References: UniProt: P13299, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, MES, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2MES11
3glycerol11
Crystal grow
*PLUS
Temperature: 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
218 %PEG33501reservoir
315 %1reservoir
40.06 MMES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11.2
SYNCHROTRONNSLS X12C21.55
Detector
TypeIDDetectorDate
BRANDEIS - B11CCDSep 20, 1999
BRANDEIS - B12CCDSep 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.551
ReflectionResolution: 2.2→30 Å / Num. all: 88623 / Num. obs: 17561 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.02 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.8 / % possible all: 98.8
Reflection
*PLUS
Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1519 -random
Rwork0.215 ---
all-17561 --
obs-15495 98.2 %-
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 855 1 185 1823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2

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