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- PDB-4xdm: N-terminal domain of Hsp90 from Dictyostelium discoideum in compl... -

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Basic information

Entry
Database: PDB / ID: 4xdm
TitleN-terminal domain of Hsp90 from Dictyostelium discoideum in complex with Geldanamycin
ComponentsHeat shock cognate 90 kDa protein
KeywordsCHAPERONE / Hsp90 / Geldanamycin
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 / protein-containing complex / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / 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 / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GELDANAMYCIN / DI(HYDROXYETHYL)ETHER / Heat shock cognate 90 kDa protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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)29,8943
Polymers29,2271
Non-polymers6672
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint2 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.400, 44.630, 60.160
Angle α, β, γ (deg.)90.00, 107.93, 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): Rosetta / References: UniProt: P54651
#2: Chemical ChemComp-GDM / GELDANAMYCIN


Mass: 560.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.81 Å3/Da / Density % sol: 32.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, PEG 3350 / PH range: 7.0 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.5→57.24 Å / Num. obs: 33584 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCJ

4xcj


Resolution: 1.5→57.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.317 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22426 1703 5.1 %RANDOM
Rwork0.18165 ---
obs0.18376 31865 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0.46 Å2
2--1.28 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 44 141 1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9912417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18225.92176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83415330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.94155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021303
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.51083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.521759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2083700
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4344.5652
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.01131783
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 123 -
Rwork0.277 2356 -
obs--100 %

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