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Yorodumi- PDB-1fyk: SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fyk | |||||||||
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Title | SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA THAT IS TRANSLATIONALLY DISORDERED | |||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / crystal-packing interface / crystallization / protein-DNA interface / protein-protein interface / static disorder / TRANSCRIPTION-DNA COMPLEX | |||||||||
Function / homology | Function and homology information protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Kluyveromyces lactis (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Littlefield, O. / Nelson, H.C.M. | |||||||||
Citation | Journal: Proteins / Year: 2001 Title: Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex. Authors: Littlefield, O. / Nelson, H.C. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: A new use for the 'wing' of the 'winged' helix-turn-helix motif in the HSF-DNA cocrystal Authors: Littlefield, O. / Nelson, H.C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyk.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyk.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyk ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | protein and DNA are not interacting in a physiologically relevant manner |
-Components
#1: DNA chain | Mass: 739.422 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence is based on an idealized HSE sequence. |
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#2: Protein | Mass: 11090.966 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: N282R, F283H, K284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) / Plasmid: PHN280R / Production host: Escherichia coli (E. coli) / References: UniProt: P22121 |
#3: 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: 2.88 Å3/Da / Density % sol: 57.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, Cacodylate, Ammonium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL1-5 / Wavelength: 0.99981 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99981 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 4940 / Num. obs: 4940 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / % possible all: 89.2 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 89.2 % / Mean I/σ(I) obs: 5.8 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The structure was originally refined by mistake with methionine in lieu of selenomethionine. The deposited coordinates have been adjusted to contain selenomethionine. Because the refinement ...Details: The structure was originally refined by mistake with methionine in lieu of selenomethionine. The deposited coordinates have been adjusted to contain selenomethionine. Because the refinement used group B-factors, the B-factors were kept the same.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.209 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rfactor Rfree: 0.358 / Num. reflection Rfree: 54 / Num. reflection Rwork: 419 / Rfactor obs: 0.308 |