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

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Basic information

Entry
Database: PDB / ID: 1fyl
TitleSERENDIPITOUS CRYSTAL STRUCTURE CONTAINING THE HEAT SHOCK TRANSCRIPTION FACTOR'S DNA BINDING DOMAIN AND COGNATE DNA IN A HEAD-TO-HEAD ORIENTATION
Components
  • HEAD-TO-HEAD HSE
  • HEAT SHOCK FACTOR PROTEIN
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 / 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 / Resolution: 2.1 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 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_ref_seq_dif.details
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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
C: HEAD-TO-HEAD HSE
D: HEAD-TO-HEAD HSE
A: HEAT SHOCK FACTOR PROTEIN
B: HEAT SHOCK FACTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,6364
Polymers29,6364
Non-polymers00
Water2,414134
1
A: HEAT SHOCK FACTOR PROTEIN

A: HEAT SHOCK FACTOR PROTEIN

C: HEAD-TO-HEAD HSE

C: HEAD-TO-HEAD HSE


Theoretical massNumber of molelcules
Total (without water)29,6364
Polymers29,6364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_565-x,y+1,-z1
Buried area1490 Å2
ΔGint-15 kcal/mol
Surface area15770 Å2
MethodPISA
2
B: HEAT SHOCK FACTOR PROTEIN

B: HEAT SHOCK FACTOR PROTEIN

D: HEAD-TO-HEAD HSE

D: HEAD-TO-HEAD HSE


Theoretical massNumber of molelcules
Total (without water)29,6364
Polymers29,6364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_566-x,y+1,-z+11
Buried area2330 Å2
ΔGint-22 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.140, 33.730, 77.840
Angle α, β, γ (deg.)90.00, 118.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain HEAD-TO-HEAD HSE


Mass: 3727.274 Da / Num. of mol.: 2 / 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.: 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.: 134 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Cacodylate, Ammonium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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: 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: 2.1→20 Å / Num. all: 12494 / Num. obs: 12494 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.164 / % possible all: 74.4
Reflection
*PLUS
% possible obs: 87 %
Reflection shell
*PLUS
% possible obs: 74.4 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3 1230 RANDOM
Rwork0.213 --
all-12490 -
obs-12490 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 484 2 134 1995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.364
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.213 / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / Rfactor Rfree: 0.366 / Num. reflection Rfree: 118 / Num. reflection Rwork: 939 / Rfactor obs: 0.279

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