+Open data
-Basic information
Entry | Database: PDB / ID: 1exn | ||||||
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Title | T5 5'-EXONUCLEASE | ||||||
Components | 5'-EXONUCLEASE | ||||||
Keywords | NUCLEASE / HYDROLASE / EXONUCLEASE | ||||||
Function / homology | Function and homology information viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / DNA exonuclease activity / double-stranded DNA endonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication ...viral replication complex / exodeoxyribonuclease (lambda-induced) / late viral transcription / DNA replication, Okazaki fragment processing / double-stranded DNA 5'-3' DNA exonuclease activity / DNA exonuclease activity / double-stranded DNA endonuclease activity / 5'-flap endonuclease activity / 5'-3' exonuclease activity / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 5'-3' DNA exonuclease activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T5 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Ceska, T.A. / Sayers, J.R. / Stier, G. / Suck, D. | ||||||
Citation | Journal: Nature / Year: 1996 Title: A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. Authors: Ceska, T.A. / Sayers, J.R. / Stier, G. / Suck, D. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Preliminary Crystallographic Studies on the D15 5' to 3' Exonuclease from Phage T5 Authors: Ceska, T.A. / Sayers, J.R. / Eckstein, F. / Suck, D. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Properties of Overexpressed Phage T5 D15 Exonuclease. Similarities with Escherichia Coli DNA Polymerase I 5'-3' Exonuclease Authors: Sayers, J.R. / Eckstein, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1exn.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1exn.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 1exn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1exn_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
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Full document | 1exn_full_validation.pdf.gz | 392 KB | Display | |
Data in XML | 1exn_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1exn_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/1exn ftp://data.pdbj.org/pub/pdb/validation_reports/ex/1exn | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33595.141 Da / Num. of mol.: 2 / Mutation: SEMET LABELLED PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T5 (virus) / Genus: T5-like viruses / Gene: D15 / Plasmid: PDOC55 / Gene (production host): D15 / Production host: Escherichia coli (E. coli) / Strain (production host): LE392 References: UniProt: P06229, exodeoxyribonuclease (lambda-induced) #2: Water | ChemComp-HOH / | Sequence details | THE N-TERMINAL MET IS REMOVED IN E. COLI. THE GENE SEQUENCE STARTING FROM RESIDUE 1 IS USED AS THE ...THE N-TERMINAL MET IS REMOVED IN E. COLI. THE GENE SEQUENCE STARTING FROM RESIDUE 1 IS USED AS THE NUMBERING SEQUENCE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Ceska, T.A., (1993) J.Mol.Biol., 233, 179. / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BL19 / Wavelength: 0.87 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Num. obs: 26463 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.037 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 67552 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 0 / Details: RESIDUE GLU A 290 IS IN POORLY DEFINED DENSITY.
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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