+Open data
-Basic information
Entry | Database: PDB / ID: 1z56 | ||||||
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Title | Co-Crystal Structure of Lif1p-Lig4p | ||||||
Components |
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Keywords | LIGASE / DNA Repair / BRCT / NHEJ / Xrcc4 / DNA Ligase / Coiled-coil | ||||||
Function / homology | Function and homology information DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase (ATP) / DNA ligase (ATP) activity / cell cycle / nucleotide-excision repair, DNA gap filling / DNA biosynthetic process / double-strand break repair via nonhomologous end joining / DNA replication / DNA recombination ...DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase (ATP) / DNA ligase (ATP) activity / cell cycle / nucleotide-excision repair, DNA gap filling / DNA biosynthetic process / double-strand break repair via nonhomologous end joining / DNA replication / DNA recombination / cell division / chromatin binding / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.92 Å | ||||||
Authors | Dore, A.S. / Furnham, N. / Davies, O.R. / Sibanda, B.L. / Chirgadze, D.Y. / Jackson, S.P. / Pellegrini, L. / Blundell, T.L. | ||||||
Citation | Journal: DNA REPAIR / Year: 2006 Title: Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. Authors: Dore, A.S. / Furnham, N. / Davies, O.R. / Sibanda, B.L. / Chirgadze, D.Y. / Jackson, S.P. / Pellegrini, L. / Blundell, T.L. | ||||||
History |
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Remark 999 | SEQUENCE As stated by the authors, the residues in chains D,E, F,G,H,I,J,K could not be aligned ... SEQUENCE As stated by the authors, the residues in chains D,E, F,G,H,I,J,K could not be aligned with any region of the two chains A and B due to low electron density and therefore have been labeled UNK. | ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DEFINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DEFINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z56.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z56.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z56_validation.pdf.gz | 487.1 KB | Display | wwPDB validaton report |
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Full document | 1z56_full_validation.pdf.gz | 550.1 KB | Display | |
Data in XML | 1z56_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 1z56_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z56 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z56 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Ligase interacting factor ... , 8 types, 10 molecules ABDEHFGIJK
#1: Protein | Mass: 28674.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P53150 #3: Protein/peptide | | Mass: 698.854 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #4: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 2 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #5: Protein/peptide | | Mass: 3847.734 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #6: Protein/peptide | | Mass: 3166.895 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #7: Protein/peptide | | Mass: 2571.161 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #8: Protein/peptide | | Mass: 1720.111 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) #9: Protein/peptide | | Mass: 1124.378 Da / Num. of mol.: 1 / Fragment: uncharacterized fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LIF1 / Production host: Escherichia coli (E. coli) |
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-Protein , 1 types, 1 molecules C
#2: Protein | Mass: 30366.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DNL4, LIG4 / Plasmid: pGAT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08387, DNA ligase (ATP) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl, Sodium Chloride, Dithiothreitol, PEG 6000, 2-(N-morpholino)ethanesulfonic acid, Ethylene Glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.968 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 20, 2004 / Details: SI-111 DOUBLE MONOCHROMATOR |
Radiation | Monochromator: SI-111 DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 3.92→49.2 Å / Num. all: 16493 / Num. obs: 16475 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 10.1 % / Rmerge(I) obs: 0.175 / Rsym value: 0.175 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.92→3.99 Å / Rmerge(I) obs: 0.799 / Rsym value: 0.799 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3.92→49.2 Å / Cor.coef. Fo:Fc: 0.75 / Cor.coef. Fo:Fc free: 0.659 / SU B: 70.148 / SU ML: 1.06 / Cross valid method: THROUGHOUT / ESU R Free: 0.961 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 107.705 Å2
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Refinement step | Cycle: LAST / Resolution: 3.92→49.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.92→4.02 Å / Total num. of bins used: 20
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