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Yorodumi- PDB-1fym: SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fym | ||||||
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Title | SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A TAIL-TO-TAIL ORIENTATION | ||||||
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 / cellular response to heat / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 | 1fym.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fym.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fym ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fym | HTTPS FTP |
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-Related 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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Details | protein and DNA are not interacting in a physiologically relevant manner |
-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence is based on an idealized HSE sequence. #2: Protein | Mass: 10950.279 Da / Num. of mol.: 2 / 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 / | |
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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: 2.09 Å3/Da / Density % sol: 41.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, Isopropanol, Cacodylate, Ammonium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / 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: BL7-1 / Wavelength: 1.02 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 10644 / Num. obs: 10644 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.186 / % possible all: 72.7 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 72.7 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The structure was originally refined by mistake with a glutamate at position 273. The deposited coordinates have been adjusted to contain aspartate at position 273, with the OD1 and OD2 ...Details: The structure was originally refined by mistake with a glutamate at position 273. The deposited coordinates have been adjusted to contain aspartate at position 273, with the OD1 and OD2 atoms having an arbitrary B-factor of 20.
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Refinement step | Cycle: LAST / Resolution: 2.2→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: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.211 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.372 / Num. reflection Rfree: 77 / Num. reflection Rwork: 733 / Rfactor obs: 0.29 |