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- PDB-3u67: Crystal structure of the N-terminal domain of Hsp90 from Leishman... -

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Basic information

Entry
Database: PDB / ID: 3u67
TitleCrystal structure of the N-terminal domain of Hsp90 from Leishmania major(LmjF33.0312)in complex with ADP
ComponentsHeat shock protein 83-1
KeywordsCHAPERONE / Structural Genomics / Structural Genomics Consortium / SGC / ATPase / ATP binding
Function / homology
Function and homology information


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 / nucleoplasm / ATP binding ...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 / nucleoplasm / ATP binding / metal ion binding / 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-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
ADENOSINE-5'-DIPHOSPHATE / Heat shock protein 83-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsPizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. ...Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS Negl Trop Dis / Year: 2013
Title: Exploring the Trypanosoma brucei Hsp83 potential as a target for structure guided drug design.
Authors: Pizarro, J.C. / Hills, T. / Senisterra, G. / Wernimont, A.K. / Mackenzie, C. / Norcross, N.R. / Ferguson, M.A. / Wyatt, P.G. / Gilbert, I.H. / Hui, R.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7486
Polymers26,1101
Non-polymers6385
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock protein 83-1
hetero molecules

A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49612
Polymers52,2212
Non-polymers1,27510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.865, 42.991, 51.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Heat shock protein 83-1


Mass: 26110.465 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: FRIEDLIN
Gene: HSP83, HSP83-10, HSP83-11, HSP83-12, HSP83-13, HSP83-14, HSP83-15, HSP83-16, HSP83-17, HSP83-2, HSP83-3, HSP83-5, HSP83-6, HSP83-7, HSP83-9, LMJF_33_0312, LMJF_33_0314, LMJF_33_0316, LMJF_33_ ...Gene: HSP83, HSP83-10, HSP83-11, HSP83-12, HSP83-13, HSP83-14, HSP83-15, HSP83-16, HSP83-17, HSP83-2, HSP83-3, HSP83-5, HSP83-6, HSP83-7, HSP83-9, LMJF_33_0312, LMJF_33_0314, LMJF_33_0316, LMJF_33_0320, LMJF_33_0323, LMJF_33_0326, LMJF_33_0333, LMJF_33_0336, LMJF_33_0340, LMJF_33_0343, LMJF_33_0346, LMJF_33_0350, LMJF_33_0355, LMJF_33_0360, LMJF_33_0365
Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q4I6
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1M NH4SO4, 0.1M bis-tris, 4.15mM ADP, 5mM MgCl2 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 158 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 13, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 26898 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.55 Å2 / Rsym value: 0.093 / Net I/σ(I): 18.9
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 5.8 % / Num. unique all: 2586 / Rsym value: 0.492 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3H80

3h80


Resolution: 1.77→32.94 Å / Cor.coef. Fo:Fc: 0.9293 / Cor.coef. Fo:Fc free: 0.9177 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 1349 5.02 %RANDOM
Rwork0.2024 ---
obs0.2042 26855 --
all-26898 --
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-7.2869 Å20 Å20 Å2
2--7.3168 Å20 Å2
3----14.6037 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 1.77→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 40 187 1891
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052446HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d661SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes272HARMONIC5
X-RAY DIFFRACTIONt_it1800HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion14.67
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2268SEMIHARMONIC4
LS refinement shellResolution: 1.77→1.84 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.246 136 4.87 %
Rwork0.2252 2656 -
all0.2263 2792 -

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