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- PDB-1ln0: Structure of the Catalytic Domain of Homing Endonuclease I-TevI -

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Basic information

Entry
Database: PDB / ID: 1ln0
TitleStructure of the Catalytic Domain of Homing Endonuclease I-TevI
Componentsintron-associated endonuclease 1
KeywordsHYDROLASE / alpha/beta fold
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
Nuclease associated modular domain 3 / Intron endonuclease, group I / : / Intron-encoded endonuclease 1, DNA-binding domain / Intron-associated endonuclease 1 zinc finger domain / Intron-encoded nuclease repeat 2 / GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease ...Nuclease associated modular domain 3 / Intron endonuclease, group I / : / Intron-encoded endonuclease 1, DNA-binding domain / Intron-associated endonuclease 1 zinc finger domain / Intron-encoded nuclease repeat 2 / GIY-YIG endonuclease / GIY-YIG endonuclease / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG endonuclease superfamily / GIY-YIG catalytic domain / GIY-YIG domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Intron-associated endonuclease 1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsVan Roey, P. / Meehan, L. / Kowalski, J.C. / Belfort, M. / Derbyshire, V.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.
Authors: Van Roey, P. / Meehan, L. / Kowalski, J.C. / Belfort, M. / Derbyshire, V.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: intron-associated endonuclease 1
B: intron-associated endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9484
Polymers22,7562
Non-polymers1922
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.870, 56.580, 35.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsdimer of domain covalently linked by disulfide bridge between Cys39 residues

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Components

#1: Protein intron-associated endonuclease 1 / homing endonuclease I-TevI / IRF PROTEIN


Mass: 11377.977 Da / Num. of mol.: 2 / Fragment: catalytic domain (residues 1 to 97) / Mutation: R27A
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 / Production host: Escherichia coli (E. coli)
References: UniProt: P13299, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG8000, 0.1 M MES, 5% ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
3150 mM1dropNaCl
41 mMdithiothreitol1drop
50.01 %(w/v)1dropNaN3
622 %(w/v)PEG80001reservoir
7100 mMMES1reservoirpH6.5
85 %(w/v)ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B1.2 / Detector: CCD / Date: Aug 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 16242 / Num. obs: 15982 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.73 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.4
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.3 / % possible all: 61.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 16242
Reflection shell
*PLUS
% possible obs: 61.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNS1refinement
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1593 -random
Rwork0.202 ---
all0.202 15982 --
obs0.202 15982 91 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 10 208 1797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.202
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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