+Open data
-Basic information
Entry | Database: PDB / ID: 1f39 | ||||||
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Title | CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR C-TERMINAL DOMAIN | ||||||
Components | REPRESSOR PROTEIN CI | ||||||
Keywords | VIRAL PROTEIN / COOPERATIVE OPERATOR BINDING / RECA-MEDIATED SELF-CLEAVAGE / GENE REGULATION | ||||||
Function / homology | Function and homology information maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Bell, C.E. / Frescura, P. / Hochschild, A. / Lewis, M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Crystal structure of the lambda repressor C-terminal domain provides a model for cooperative operator binding. Authors: Bell, C.E. / Frescura, P. / Hochschild, A. / Lewis, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f39.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f39.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f39 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f39 | 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 on special symmetry positions |
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Details | The biological assembly is a tetramer constructed from chains A and B and symmetry partners generated by the crystallographic 2-fold axis along a. |
-Components
#1: Protein | Mass: 10931.332 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: PET-14B / Production host: Escherichia coli (E. coli) / References: UniProt: P03034 #2: 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: 3.04 Å3/Da / Density % sol: 59.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.2 M NaH2PO4, 1.05 M KH2PO4, 0.075 M hepes, 25% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jan 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17 Å / Num. obs: 22468 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.105 / % possible all: 58.1 |
Reflection | *PLUS Num. measured all: 71961 |
Reflection shell | *PLUS % possible obs: 58.1 % / Mean I/σ(I) obs: 4.7 |
-Processing
Software |
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Refinement | Resolution: 1.9→14.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 961024.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.43 Å2 / ksol: 0.481 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→14.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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