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- PDB-1t2t: Crystal structure of the DNA-binding domain of intron endonucleas... -

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Basic information

Entry
Database: PDB / ID: 1t2t
TitleCrystal structure of the DNA-binding domain of intron endonuclease I-TevI with operator site
Components
  • 5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3'
  • 5'-D(*TP*TP*TP*GP*TP*AP*GP*GP*AP*CP*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*T)-3'
  • Intron-associated endonuclease 1
KeywordsHYDROLASE/DNA / protein-DNA complex / 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 / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsEdgell, D.R. / Derbyshire, V. / Van Roey, P. / LaBonne, S. / Stanger, M.J. / Li, Z. / Boyd, T.M. / Shub, D.A. / Belfort, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.
Authors: Edgell, D.R. / Derbyshire, V. / Van Roey, P. / LaBonne, S. / Stanger, M.J. / Li, Z. / Boyd, T.M. / Shub, D.A. / Belfort, M.
History
DepositionApr 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
B: 5'-D(*TP*TP*TP*GP*TP*AP*GP*GP*AP*CP*TP*GP*CP*CP*CP*TP*TP*TP*AP*AP*T)-3'
C: 5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3'
A: Intron-associated endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1914
Polymers26,1263
Non-polymers651
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.660, 64.890, 42.810
Angle α, β, γ (deg.)90.00, 90.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6419.155 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*TP*TP*AP*AP*AP*GP*GP*GP*CP*AP*GP*TP*CP*CP*TP*AP*CP*AP*A)-3'


Mass: 6464.225 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Intron-associated endonuclease 1 / I-TevI / IRF protein


Mass: 13242.219 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (residues 130-245)
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 / Gene: ITEVIR / 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.: 72 / 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: 2.91 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, glycerol, sodium formate, sodium chloride, PEG 3350, isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2glycerol11
3sodium formate11
4sodium chloride11
5PEG11
6isopropanol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 10240 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1I3J

1i3j


Resolution: 2.5→29.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 225915.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 956 10.2 %RANDOM
Rwork0.238 ---
obs0.238 9349 89.6 %-
all-10240 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.406 Å2 / ksol: 0.334445 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.36 Å20 Å2-12.9 Å2
2--11.3 Å20 Å2
3----2.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 855 1 72 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.83
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.122.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 143 10.7 %
Rwork0.359 1197 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP

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