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- PDB-1bgq: RADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1bgq
TitleRADICICOL BOUND TO THE ATP BINDING SITE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE
ComponentsHEAT SHOCK PROTEIN 90
KeywordsCHAPERONE / ATP-BINDING / HEAT SHOCK / INHIBITOR
Function / homology
Function and homology information


The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / regulation of telomere maintenance / protein targeting to mitochondrion / response to osmotic stress / 'de novo' protein folding / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / protein maturation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RADICICOL / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.5 Å
AuthorsRoe, S.M. / Prodromou, C. / Pearl, L.H.
Citation
Journal: J.Med.Chem. / Year: 1999
Title: Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin.
Authors: Roe, S.M. / Prodromou, C. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Identification and Structural Characterization of the ATP/Adp-Binding Site in the Hsp90 Molecular Chaperone
Authors: Prodromou, C. / Roe, S.M. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H.
#2: Journal: Proteins / Year: 1996
Title: Expression and Crystallization of the Yeast Hsp82 Chaperone, and Preliminary X-Ray Diffraction Studies of the Amino-Terminal Domain
Authors: Prodromou, C. / Piper, P.W. / Pearl, L.H.
History
DepositionMay 29, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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
A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8922
Polymers25,5271
Non-polymers3651
Water1,69394
1
A: HEAT SHOCK PROTEIN 90
hetero molecules

A: HEAT SHOCK PROTEIN 90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7844
Polymers51,0542
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)73.940, 73.940, 110.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein HEAT SHOCK PROTEIN 90 / HSP90


Mass: 25527.037 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P02829
#2: Chemical ChemComp-RDC / RADICICOL / MONORDEN


Mass: 364.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17ClO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.97 Å3/Da / Density % sol: 60 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein11
29.75 %(w/v)mPEG55011
365 mMammonium sulfate11
432.5 mMsodium succinate11
525 %(v/v)glycerol11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11672 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.073 / Net I/σ(I): 8.4
Reflection shellResolution: 2.46→2.58 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.233 / % possible all: 99.1
Reflection
*PLUS
Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.233

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: 1AH6

1ah6


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 577 5.2 %RANDOM
Rwork0.2 ---
obs0.2 11170 99.8 %-
Displacement parametersBiso mean: 24.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 25 94 1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.92
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.441.5
X-RAY DIFFRACTIONx_mcangle_it3.782
X-RAY DIFFRACTIONx_scbond_it4.252
X-RAY DIFFRACTIONx_scangle_it6.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 96 5.3 %
Rwork0.253 1717 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2RDC.PARWATER.TOP
X-RAY DIFFRACTION3WATER.PARRDC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.92

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