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- PDB-3hts: HEAT SHOCK TRANSCRIPTION FACTOR/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3hts
TitleHEAT SHOCK TRANSCRIPTION FACTOR/DNA COMPLEX
Components
  • 5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'
  • HEAT SHOCK TRANSCRIPTION FACTOR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / COMPLEX (WINGED HELIX_TURN_ HELIX-DNA) / 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
Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLittlefield, O. / Nelson, H.C.M.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Refinedsolution Structure and Dynamics of the DNA-Binding Domain of the Heat Shock Factor from Kluyveromyces Lactis
Authors: Damberger, F.F. / Pelton, J.G. / Liu, C. / Cho, H. / Harrison, C.J. / Nelson, H.C.M. / Wemmer, D.E.
#2: Journal: Science / Year: 1994
Title: Crystal Structure of the DNA Binding Domain of the Heat Shock Transcription Factor
Authors: Harrison, C.J. / Bohm, A.A. / Nelson, H.C.M.
History
DepositionNov 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'
B: HEAT SHOCK TRANSCRIPTION FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6963
Polymers15,6042
Non-polymers921
Water1,26170
1
A: 5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'
B: HEAT SHOCK TRANSCRIPTION FACTOR
hetero molecules

A: 5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'
B: HEAT SHOCK TRANSCRIPTION FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3926
Polymers31,2084
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)62.690, 54.900, 41.060
Angle α, β, γ (deg.)90.00, 122.44, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-19-

HOH

21A-24-

HOH

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Components

#1: DNA chain 5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3' / TAIL-TO-TAIL HEAT SHOCK ELEMENT


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DESIGN BASED UPON HEAT SHOCK ELEMENT CONSENSUS SEQUENCE
#2: Protein HEAT SHOCK TRANSCRIPTION FACTOR


Mass: 11941.409 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN (RESIDUES 193-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22121
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.89 Å3/Da / Density % sol: 35.02 %
Description: LOW RESOLUTION DATA WERE COLLECTED ON A ROTATING ANODE
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.91 mMprotein1drop
21.47 mMDNA1drop
315 %(v/v)isopropanol1reservoir
450 mMHEPES1reservoir
520 mM1reservoirMgCl2
6100 mMpotassium glutamate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.75→27.5 Å / Num. obs: 10653 / % possible obs: 89.4 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 10.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 7.4 / % possible all: 86
Reflection
*PLUS
Num. measured all: 34273
Reflection shell
*PLUS
% possible obs: 86 % / Num. unique obs: 750 / Num. measured obs: 1928

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HTS

2hts


Resolution: 1.75→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1120 10.5 %RANDOM
Rwork0.208 ---
all-10644 --
obs-10644 89.1 %-
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--13 Å20 Å2-2.58 Å2
2--6.43 Å20 Å2
3---6.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 243 6 70 1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.371.5
X-RAY DIFFRACTIONx_mcangle_it5.372
X-RAY DIFFRACTIONx_scbond_it4.472
X-RAY DIFFRACTIONx_scangle_it6.152
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 160 9.5 %
Rwork0.323 1532 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4GLYCEROL.PARAMGLYCEROL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.001
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.85
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.323 / Rfactor obs: 0.323

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