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- PDB-1u0d: Y33H Mutant of Homing endonuclease I-CreI -

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Basic information

Entry
Database: PDB / ID: 1u0d
TitleY33H Mutant of Homing endonuclease I-CreI
Components
  • 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
  • DNA endonuclease I-CreI
KeywordsHYDROLASE/dna / DNA endonuclease I-CreI / PROTEIN/dna / HYDROLASE-dna COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSussman, D. / Chadsey, M. / Fauce, S. / Engel, A. / Bruett, A. / Monnat, R. / Stoddard, B.L. / Seligman, L.M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Isolation and characterization of new homing endonuclease specificities at individual target site positions.
Authors: Sussman, D. / Chadsey, M. / Fauce, S. / Engel, A. / Bruett, A. / Monnat, R. / Stoddard, B.L. / Seligman, L.M.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
D: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3'
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI


Theoretical massNumber of molelcules
Total (without water)52,1394
Polymers52,1394
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.838, 70.331, 88.016
Angle α, β, γ (deg.)90.28, 89.94, 98.78
Int Tables number1
Space group name H-MP1
Number of models2

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Components

#1: DNA chain 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'


Mass: 7419.792 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3'


Mass: 7321.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA endonuclease I-CreI / 3.1.-.- / 23S rRNA intron protein


Mass: 18698.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli)
References: UniProt: P05725, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 76.09 %

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Data collection

DetectorDate: Aug 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→29.5 Å / Num. obs: 21529

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.5 Å / σ(F): 0
RfactorNum. reflection
Rfree0.2565 2132
Rwork0.2174 -
all0.256 -
obs0.242 21529
Refinement stepCycle: LAST / Resolution: 2.9→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 978 0 0 3446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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