+Open data
-Basic information
Entry | Database: PDB / ID: 1ut5 | ||||||
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Title | Divalent metal ions (manganese) bound to T5 5'-exonuclease | ||||||
Components | EXODEOXYRIBONUCLEASE | ||||||
Keywords | HYDROLASE / EXONUCLEASE / NUCLEASE | ||||||
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 | BACTERIOPHAGE T5 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ceska, T.A. / Sayers, J.R. / Suck, D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Roles of Divalent Metal Ions in Flap Endonuclease-Substrate Interactions Authors: Feng, M. / Patel, D. / Dervan, J. / Ceska, T.A. / Suck, D. / Haq, I. / Sayers, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ut5.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ut5.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ut5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1ut5 ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1ut5 | HTTPS FTP |
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-Related structure data
Related structure data | 1ut8C 1exnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 33491.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE T5 (virus) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P06229, exodeoxyribonuclease (lambda-induced) #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.03 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: 35% AMMONIUM SULFATE 100MM SODIUM CITRATE PH 5.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Ceska, T.A., (1993) J.Mol.Biol., 233, 179. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Nov 15, 1996 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. obs: 19024 / % possible obs: 74.6 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.041 |
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Num. obs: 16150 / Num. measured all: 19024 / Rmerge(I) obs: 0.041 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EXN Resolution: 2.75→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: MASK / Bsol: 76.6 Å2 / ksol: 0.415 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |