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Yorodumi- PDB-1dml: CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dml | ||||||
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Title | CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/TRANSFERASE / herpes simplex virus / dna synthesis / sliding clamps / PCNA / processivity / DNA BINDING PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / ribonuclease H / DNA polymerase processivity factor activity / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding ...DNA polymerase complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / ribonuclease H / DNA polymerase processivity factor activity / RNA-DNA hybrid ribonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / host cell nucleus / DNA binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Zuccola, H.J. / Filman, D.J. / Coen, D.M. / Hogle, J.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase. Authors: Zuccola, H.J. / Filman, D.J. / Coen, D.M. / Hogle, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dml.cif.gz | 238.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dml.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dml ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dml | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a heterodimer of UL42 and HSV Polymerase |
-Components
#1: Protein | Mass: 34231.879 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Genus: Simplexvirus / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / References: UniProt: P10226 #2: Protein/peptide | Mass: 3751.197 Da / Num. of mol.: 4 / Fragment: C-TERMINAL 36 AMINO ACIDS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Genus: Simplexvirus / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07917, DNA-directed DNA polymerase |
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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: 2.28 Å3/Da / Density % sol: 45.97 % | |||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: PEGMME 5000, pH 7.5, vapor diffusion, temperature 22K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.87 Å / Num. all: 37576 / Num. obs: 37917 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.244 / Num. unique all: 37217 / % possible all: 99.8 |
Reflection | *PLUS Num. obs: 37576 / Num. measured all: 260475 |
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 6.1 |
-Processing
Software |
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Refinement | Resolution: 2.7→12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3153280.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.41 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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