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- PDB-1byq: HSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG -

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Entry
Database: PDB / ID: 1byq
TitleHSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG
ComponentsPROTEIN (HEAT SHOCK PROTEIN 90)
KeywordsCHAPERONE / CHAPERONE PROTEIN / ATP BINDING
Function / homologyHsp90 protein / vRNP Assembly / Loss of Nlp from mitotic centrosomes / HSF1-dependent transactivation / Attenuation phase / HSF1 activation / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Scavenging by Class F Receptors / Regulation of PLK1 Activity at G2/M Transition / eNOS activation ...Hsp90 protein / vRNP Assembly / Loss of Nlp from mitotic centrosomes / HSF1-dependent transactivation / Attenuation phase / HSF1 activation / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Scavenging by Class F Receptors / Regulation of PLK1 Activity at G2/M Transition / eNOS activation / Regulation of actin dynamics for phagocytic cup formation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of proteins required for interphase microtubule organization from the centrosome / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by ERBB2 / Heat shock hsp90 proteins family signature. / Heat shock protein Hsp90 family / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90, conserved site / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, N-terminal / Histidine kinase/HSP90-like ATPase superfamily / HSP90, C-terminal domain / Recruitment of mitotic centrosome proteins and complexes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / AURKA Activation by TPX2 / Downregulation of ERBB2 signaling / Interleukin-4 and Interleukin-13 signaling / Neutrophil degranulation / VEGFA-VEGFR2 Pathway / The role of GTSE1 in G2/M progression after G2 checkpoint / Uptake and function of diphtheria toxin / Sema3A PAK dependent Axon repulsion / ESR-mediated signaling / VEGFR2 mediated vascular permeability / Recruitment of NuMA to mitotic centrosomes / Constitutive Signaling by EGFRvIII / PIWI-interacting RNA (piRNA) biogenesis / Estrogen-dependent gene expression / Anchoring of the basal body to the plasma membrane / positive regulation of protein polymerization / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / mitochondrial transport / chaperone-mediated autophagy / positive regulation of cellular protein catabolic process / TPR domain binding / dendritic growth cone / chaperone-mediated protein complex assembly / central nervous system neuron axonogenesis / cofactor metabolic process / axon extension / protein unfolding / telomere maintenance via telomerase / regulation of protein complex assembly / regulation of protein ubiquitination / DNA polymerase binding / regulation of cellular protein localization / protein tyrosine kinase binding / positive regulation of tau-protein kinase activity / MHC class II protein complex binding / GTPase binding / axonal growth cone / ciliary basal body-plasma membrane docking / endocytic vesicle lumen / establishment of cell polarity / response to unfolded protein / regulation of nitric-oxide synthase activity / positive regulation of telomerase activity / response to cold / ATPase activity, coupled / lysosomal lumen / ERBB2 signaling pathway / nitric-oxide synthase regulator activity / tau protein binding / regulation of cellular response to heat / melanosome / histone deacetylase binding / vascular endothelial growth factor receptor signaling pathway / receptor-mediated endocytosis / regulation of G2/M transition of mitotic cell cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / scaffold protein binding / unfolded protein binding / cellular response to heat / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to heat / G2/M transition of mitotic cell cycle / protein stabilization / secretory granule lumen / protein refolding / ficolin-1-rich granule lumen / ATPase activity / protein tyrosine kinase activity / positive regulation of protein phosphorylation / positive regulation of protein kinase B signaling / myelin sheath / response to antibiotic
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.5 Å resolution
AuthorsRusso, A.A. / Pavletich, N.P.
CitationJournal: J.Cell Biol. / Year: 1998
Title: In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis.
Authors: Obermann, W.M. / Sondermann, H. / Russo, A.A. / Pavletich, N.P. / Hartl, F.U.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 19, 1998 / Release: Oct 28, 1998
RevisionDateData content typeGroupProviderType
1.0Oct 28, 1998Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEAT SHOCK PROTEIN 90)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1223
Polyers25,6711
Non-polymers4522
Water6,918384
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)53.140, 42.500, 53.960
Angle α, β, γ (deg.)90.00, 115.53, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide PROTEIN (HEAT SHOCK PROTEIN 90) / HSP90


Mass: 25670.795 Da / Num. of mol.: 1 / Fragment: RESIDUES 9 - 236 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Plasmid name: PET3D / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Formula: H2O / Water

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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: 2.14 / Density percent sol: 42.56 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Method: unknown
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mMATPgammaS11
20.2 Mmagnesium chloride11
30.1 MTris-HCl11
430 %PEG400011

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Data collection

DiffractionMean temperature: 108 kelvins
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE A1 / Synchrotron site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorCollection date: Jul 4, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionD resolution high: 1.5 Å / D resolution low: 2 Å / Number obs: 33303 / Observed criterion sigma I: 0 / Rmerge I obs: 0.059 / Redundancy: 3.5 % / Percent possible obs: 95.1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YES
R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Least-squares processR factor R free: 0.247 / R factor R work: 0.189 / R factor obs: 0.189 / Highest resolution: 1.5 Å / Lowest resolution: 1 Å / Number reflection R free: 1600 / Number reflection obs: 31430 / Percent reflection R free: 4.6 / Percent reflection obs: 90.1
Refine hist #LASTHighest resolution: 1.5 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1678 / Nucleic acid: 0 / Ligand: 28 / Solvent: 384 / Total: 2090
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.60
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.60
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it6.50
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO

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