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- PDB-2xd6: Hsp90 complexed with a resorcylic acid macrolactone. -

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Basic information

Entry
Database: PDB / ID: 2xd6
TitleHsp90 complexed with a resorcylic acid macrolactone.
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE / INHIBITOR / ATPASE
Function / homology
Function and homology information


The NLRP3 inflammasome / HSF1-dependent transactivation / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / protein maturation / protein targeting to mitochondrion ...The NLRP3 inflammasome / HSF1-dependent transactivation / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / protein maturation / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / 'de novo' protein folding / response to osmotic stress / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / ATP hydrolysis activity / perinuclear region of cytoplasm / protein-containing complex / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90, conserved site / Heat shock protein Hsp90, N-terminal / HSP90, C-terminal domain / Hsp90 protein / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90, conserved site / Heat shock protein Hsp90, N-terminal / HSP90, C-terminal domain / Hsp90 protein / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-like ATPases / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
Chem-XD6 / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRoe, S.M. / Prodromou, C. / Pearl, L.H. / Moody, C.J.
CitationJournal: Chemistry / Year: 2010
Title: Inhibition of Hsp90 with Resorcylic Acid Macrolactones. Synthesis and Binding Studies.
Authors: Day, J.E.H. / Sharp, S.Y. / Rowlands, M.G. / Aherne, W. / Lewis, W. / Roe, S.M. / Prodromou, C. / Pearl, L.H. / Workman, P. / Moody, C.J.
History
DepositionApr 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2May 1, 2013Group: Non-polymer description / Refinement description / Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9446
Polymers24,2091
Non-polymers7355
Water3,909217
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,88812
Polymers48,4172
Non-polymers1,47010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area4220 Å2
ΔGint-8.8 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.767, 73.767, 110.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

21A-2067-

HOH

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Components

#1: Protein ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN / HSP90


Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Chemical ChemComp-XD6 / (5Z)-13-CHLORO-14,16-DIHYDROXY-1,11-DIOXO-3,4,7,8,9,10,11,12-OCTAHYDRO-1H-2-BENZOXACYCLOTETRADECINE-6-CARBALDEHYDE / RESORCYCLIC ACID MACROLACTONE


Mass: 366.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19ClO6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.12 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Dec 3, 2009 / Details: HELIOS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 16104 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SAINTdata reduction
XPREPdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AH6
Resolution: 2.2→31.606 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 804 5 %
Rwork0.1701 --
obs0.1728 16061 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.893 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8429 Å2-0 Å20 Å2
2---0.8429 Å2-0 Å2
3---1.6858 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 49 217 1946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071764
X-RAY DIFFRACTIONf_angle_d1.052378
X-RAY DIFFRACTIONf_dihedral_angle_d16.124667
X-RAY DIFFRACTIONf_chiral_restr0.069272
X-RAY DIFFRACTIONf_plane_restr0.005303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33790.26431280.18772469X-RAY DIFFRACTION100
2.3379-2.51830.25141280.17452482X-RAY DIFFRACTION100
2.5183-2.77160.23661690.17522475X-RAY DIFFRACTION100
2.7716-3.17230.23961360.16852524X-RAY DIFFRACTION100
3.1723-3.99560.23791420.15962556X-RAY DIFFRACTION100
3.9956-31.60910.17661010.16932751X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.3586 Å / Origin y: 5.7208 Å / Origin z: 0.6959 Å
111213212223313233
T0.0625 Å20.0032 Å20.0115 Å2-0.0597 Å2-0.0111 Å2--0.0803 Å2
L1.4404 °20.0186 °2-0.0106 °2-0.6562 °2-0.0901 °2--0.5364 °2
S-0.0637 Å °0.0107 Å °0.0956 Å °-0.0046 Å °-0.0183 Å °-0.0787 Å °0.0205 Å °0.0003 Å °0.0737 Å °
Refinement TLS groupSelection details: ALL

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