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- PDB-6cjj: Candida albicans Hsp90 nucleotide binding domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6cjj
TitleCandida albicans Hsp90 nucleotide binding domain in complex with ADP
ComponentsHeat shock protein 90 homologHeat shock response
KeywordsCHAPERONE / Hsp90. ATPase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / intracellular steroid hormone receptor signaling pathway / ATP-dependent protein folding chaperone / extracellular vesicle / unfolded protein binding / protein folding ...negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / intracellular steroid hormone receptor signaling pathway / ATP-dependent protein folding chaperone / extracellular vesicle / unfolded protein binding / protein folding / cellular response to heat / regulation of apoptotic process / protein stabilization / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...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-, DNA gyrase B-, and HSP90-like ATPase / 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
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHutchinson, A. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / STRUCTURAL GENOMICS CONSORTIUM, S.G.C. / Pizarro, J.C. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for species-selective targeting of Hsp90 in a pathogenic fungus.
Authors: Whitesell, L. / Robbins, N. / Huang, D.S. / McLellan, C.A. / Shekhar-Guturja, T. / LeBlanc, E.V. / Nation, C.S. / Hui, R. / Hutchinson, A. / Collins, C. / Chatterjee, S. / Trilles, R. / Xie, ...Authors: Whitesell, L. / Robbins, N. / Huang, D.S. / McLellan, C.A. / Shekhar-Guturja, T. / LeBlanc, E.V. / Nation, C.S. / Hui, R. / Hutchinson, A. / Collins, C. / Chatterjee, S. / Trilles, R. / Xie, J.L. / Krysan, D.J. / Lindquist, S. / Porco Jr., J.A. / Tatu, U. / Brown, L.E. / Pizarro, J. / Cowen, L.E.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8717
Polymers26,2091
Non-polymers6626
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.088, 74.088, 107.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21A-586-

HOH

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Components

#1: Protein Heat shock protein 90 homolog / Heat shock response


Mass: 26208.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta 2 / References: UniProt: P46598
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM Hepes 2M ammonium sulfate 2% PEG 400

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 31576 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.1
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1563 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 1.74→30 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 --Random selection
Rwork0.1697 ---
obs-31153 100 %-
Displacement parametersBiso mean: 28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 41 219 1941

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