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- PDB-4xko: N-terminal domain of Hsp90 from Dictyostelium discoideum in hexag... -

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Basic information

Entry
Database: PDB / ID: 4xko
TitleN-terminal domain of Hsp90 from Dictyostelium discoideum in hexagonal form with PEG
ComponentsHeat shock cognate 90 kDa protein
KeywordsCHAPERONE / Hsp90 / PEG
Function / homology
Function and homology information


regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling / ESR-mediated signaling ...regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling / ESR-mediated signaling / Extra-nuclear estrogen signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of actin dynamics for phagocytic cup formation / Neutrophil degranulation / phagocytic vesicle / extracellular matrix / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol
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-like ATPases ...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-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
DI(HYDROXYETHYL)ETHER / Heat shock cognate 90 kDa protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å
AuthorsRaman, S. / Suguna, K.
CitationJournal: Sci Rep / Year: 2015
Title: First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90
Authors: Raman, S. / Singh, M. / Tatu, U. / Suguna, K.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock cognate 90 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4963
Polymers29,2271
Non-polymers2692
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.190, 158.190, 46.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-414-

HOH

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Components

#1: Protein Heat shock cognate 90 kDa protein / Heat shock protein 90


Mass: 29226.871 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX2 / Gene: hspD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P54651
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris, Ammonium sulphate, PEG 200 / PH range: 7.50-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.455→51.78 Å / Num. obs: 12933 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 24.2
Reflection shellResolution: 2.455→2.59 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCJ

4xcj


Resolution: 2.455→51.78 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 629 4.87 %
Rwork0.2161 --
obs0.2185 12918 99.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.47 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3578 Å2-0 Å2-0 Å2
2--7.3578 Å2-0 Å2
3----14.7156 Å2
Refinement stepCycle: LAST / Resolution: 2.455→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 18 46 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081718
X-RAY DIFFRACTIONf_angle_d1.0572316
X-RAY DIFFRACTIONf_dihedral_angle_d15.893636
X-RAY DIFFRACTIONf_chiral_restr0.068274
X-RAY DIFFRACTIONf_plane_restr0.003291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4554-2.70250.32141770.28312977X-RAY DIFFRACTION100
2.7025-3.09350.29451460.2583017X-RAY DIFFRACTION100
3.0935-3.89730.33521570.2143054X-RAY DIFFRACTION100
3.8973-51.79130.20781490.19513241X-RAY DIFFRACTION100

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