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- PDB-4xkk: Crystal structure of N-terminal domain of Hsp90 from Dictyosteliu... -

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Basic information

Entry
Database: PDB / ID: 4xkk
TitleCrystal structure of N-terminal domain of Hsp90 from Dictyostelium discoideum
ComponentsHeat shock cognate 90 kDa protein
KeywordsCHAPERONE / Hsp90 / Dictyostelium discoideum
Function / homology
Function and homology information


regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling ...regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling / Extra-nuclear estrogen signaling / 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
Heat shock cognate 90 kDa protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRaman, S. / Suguna, K.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: Heat shock protein 90 regulates development in Dictyostelium discoideum
Authors: Sawarkar, R. / Roy, N. / Rao, S. / Raman, S. / Venketesh, S. / Suguna, K. / Tatu, U.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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


Theoretical massNumber of molelcules
Total (without water)29,2271
Polymers29,2271
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10920 Å2
Unit cell
Length a, b, c (Å)41.240, 44.860, 60.249
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.82 Å3/Da / Density % sol: 32.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, PEG 3350 / PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.7→39.31 Å / Num. obs: 5876 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.2 / % possible all: 99.2

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YES

1yes


Resolution: 2.7→28.68 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.845 / SU B: 14.64 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 1.13 / ESU R Free: 0.413
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27164 267 4.6 %RANDOM
Rwork0.21817 ---
obs0.22036 5583 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.07 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 0 27 1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9682289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.33726.02773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.737155
X-RAY DIFFRACTIONr_chiral_restr0.2430.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021231
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2775
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21160
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 23 -
Rwork0.299 418 -
obs--98.66 %

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