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

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Basic information

Entry
Database: PDB / ID: 1fym
TitleSERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A TAIL-TO-TAIL ORIENTATION
Components
  • HEAT SHOCK TRANSCRIPTION PROTEIN
  • TAIL-TO-TAIL HSE
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 / DNA (> 10) / Heat shock transcription factor
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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: RCSB / Processing site: RCSB
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 1.3Dec 18, 2019Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: TAIL-TO-TAIL HSE
D: TAIL-TO-TAIL HSE
A: HEAT SHOCK TRANSCRIPTION PROTEIN
B: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water1,65792
1
C: TAIL-TO-TAIL HSE

C: TAIL-TO-TAIL HSE

A: HEAT SHOCK TRANSCRIPTION PROTEIN

A: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
2
D: TAIL-TO-TAIL HSE

D: TAIL-TO-TAIL HSE

B: HEAT SHOCK TRANSCRIPTION PROTEIN

B: HEAT SHOCK TRANSCRIPTION PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2254
Polymers29,2254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+12
crystal symmetry operation2_546-x,y-1,-z+11
Unit cell
Length a, b, c (Å)106.510, 34.020, 78.210
Angle α, β, γ (deg.)90.00, 119.31, 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 TAIL-TO-TAIL HSE


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is based on an idealized HSE sequence.
#2: Protein HEAT SHOCK TRANSCRIPTION PROTEIN / HEAT SHOCK TRANSCRIPTION FACTOR


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 / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 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
IDNameCrystal-IDSol-ID
1PEG 400011
2Isopropanol11
3Cacodylate11
4Ammonium Acetate11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
210 %isopropanol1reservoir
350 mMcacodylate1reservoir
4200 mMammonium acetate1reservoir
50.91 mMprotein1drop
60.69 mMDNA1drop
710 mMTris1drop
850 mM1dropNaCl
9400 mMammonium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.02
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 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.
RfactorNum. reflectionSelection details
Rfree0.295 1049 RANDOM
Rwork0.211 --
all-10642 -
obs-10642 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 486 0 92 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.388
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

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