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Yorodumi- PDB-1dvo: THE X-RAY CRYSTAL STRUCTURE OF FINO, A REPRESSOR OF BACTERIAL CON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dvo | ||||||
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Title | THE X-RAY CRYSTAL STRUCTURE OF FINO, A REPRESSOR OF BACTERIAL CONJUGATION | ||||||
Components | FERTILITY INHIBITION PROTEIN O | ||||||
Keywords | TRANSCRIPTION / Repressor / Bacterial Conjugation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Ghetu, A.F. / Gubbins, M.J. / Frost, L.S. / Glover, J.N.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structure of the bacterial conjugation repressor finO. Authors: Ghetu, A.F. / Gubbins, M.J. / Frost, L.S. / Glover, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dvo.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dvo.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/1dvo ftp://data.pdbj.org/pub/pdb/validation_reports/dv/1dvo | HTTPS FTP |
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-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
#1: Protein | Mass: 17374.115 Da / Num. of mol.: 1 / Mutation: L124M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / References: UniProt: P29367 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MES, Tris, EDTA, BME, NaCl, PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 109290 / Num. obs: 14726 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.767 Å2 / Rmerge(I) obs: 0.047 | |||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.109 / Num. unique all: 853 / % possible all: 87 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 87 % |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.1 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.009 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.234 / Rfactor Rwork: 0.204 |