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- PDB-1fyk: SERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCR... -

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Basic information

Entry
Database: PDB / ID: 1fyk
TitleSERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA THAT IS TRANSLATIONALLY DISORDERED
Components
  • HEAT SHOCK FACTOR PROTEIN
  • HSE DNA-PHOSPHATE BACKBONE
KeywordsTRANSCRIPTION/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
HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Heat shock transcription factor
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLittlefield, 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
DepositionOct 2, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 3, 2021Group: Database references / Derived calculations / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HSE DNA-PHOSPHATE BACKBONE
A: HEAT SHOCK FACTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,8302
Polymers11,8302
Non-polymers00
Water68538
1
C: HSE DNA-PHOSPHATE BACKBONE
A: HEAT SHOCK FACTOR PROTEIN

C: HSE DNA-PHOSPHATE BACKBONE
A: HEAT SHOCK FACTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6614
Polymers23,6614
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)103.150, 32.990, 42.570
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number5
Space group name H-MC121
Detailsprotein and DNA are not interacting in a physiologically relevant manner

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Components

#1: DNA chain HSE DNA-PHOSPHATE BACKBONE


Mass: 739.422 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is based on an idealized HSE sequence.
#2: Protein HEAT SHOCK FACTOR PROTEIN / HEAT SHOCK TRANSCRIPTION FACTOR


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 / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 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
IDNameCrystal-IDSol-ID
1PEG 400011
2Cacodylate11
3Ammonium Acetate11
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125-30 %PEG40001reservoir
250 mMcacodylate1reservoir
3275 mMammonium acetate1reservoir
40.91 mMprotein1drop
50.69 mMDNA1drop
610 mMTris1drop
750 mM1dropNaCl
8400 mMammonium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.99981
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99981 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 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.
RfactorNum. reflectionSelection details
Rfree0.278 518 RANDOM
Rwork0.209 --
all-4939 -
obs-4939 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 41 0 38 857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.593
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

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