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- PDB-3opd: Crystal Structure of the N-terminal domain of an HSP90 from Trypa... -

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Basic information

Entry
Database: PDB / ID: 3opd
TitleCrystal Structure of the N-terminal domain of an HSP90 from Trypanosoma Brucei, Tb10.26.1080 in the presence of a benzamide derivative
ComponentsHeat shock protein 83Heat shock response
KeywordsCHAPERONE / Structural Genomics / Structural Genomics Consortium / SGC / ATP binding
Function / homology
Function and homology information


response to unfolded protein / unfolded protein binding / protein folding / response to heat / protein refolding / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / 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
Chem-HIE / Heat shock protein 83
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Chamberlain, K. / Weadge, J. / Cossar, D. / Li, Y. / Kozieradzki, I. / Bochkarev, A. ...Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Chamberlain, K. / Weadge, J. / Cossar, D. / Li, Y. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Wyatt, P.G. / Fairlamb, A.H. / MacKenzie, C. / 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
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Sep 6, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 83
B: Heat shock protein 83
C: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9956
Polymers78,6013
Non-polymers1,3933
Water6,467359
1
A: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6652
Polymers26,2001
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6652
Polymers26,2001
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6652
Polymers26,2001
Non-polymers4641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.915, 72.103, 152.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein 83 / Heat shock response


Mass: 26200.381 Da / Num. of mol.: 3 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HSP83, Tb10.26.1080 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12861
#2: Chemical ChemComp-HIE / 4-[6,6-dimethyl-4-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]-2-[(cis-4-hydroxycyclohexyl)amino]benzamide


Mass: 464.481 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H27F3N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M AMMONIUM SULFATE 2% PEG400 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 24, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→29.6 Å / Num. obs: 24726 / % possible obs: 99.7 % / Biso Wilson estimate: 60.61 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.0678 / Net I/σ(I): 112.6

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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
Resolution: 2.6→29.85 Å / Cor.coef. Fo:Fc: 0.9341 / Cor.coef. Fo:Fc free: 0.9056 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1255 5.09 %RANDOM
Rwork0.1862 ---
obs0.1892 24658 --
Displacement parametersBiso mean: 56.35 Å2
Baniso -1Baniso -2Baniso -3
1-9.3158 Å20 Å20 Å2
2---8.0333 Å20 Å2
3----1.2824 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 99 359 5087
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0148182
X-RAY DIFFRACTIONt_angle_deg1.1965452
X-RAY DIFFRACTIONt_dihedral_angle_d16222
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1452
X-RAY DIFFRACTIONt_gen_planes7375
X-RAY DIFFRACTIONt_it481820
X-RAY DIFFRACTIONt_nbd45
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion17.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6735
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_contact56754
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2901 149 5.06 %
Rwork0.2325 2797 -
all0.2354 2946 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3478-0.6502-0.67131.55850.56861.74480.11050.25010.007-0.0306-0.0019-0.1051-0.0029-0.0529-0.1085-0.16390.0171-0.02130.0382-0.0565-0.1311.066421.39018.0081
22.051.0258-1.1523.1482-2.34852.74590.0366-0.07560.10380.51440.18660.0603-0.374-0.0798-0.2232-0.0390.0678-0.0217-0.05180.0632-0.211-8.29889.227240.3013
33.5497-0.1894-1.06961.3380.51532.85740.25920.21380.5442-0.0588-0.0280.1058-0.1743-0.4007-0.2311-0.16170.08810.081-0.090.0327-0.0442-31.106343.45621.932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - A|162 A|165 - A|209 }A0 - 162
2X-RAY DIFFRACTION1{ A|0 - A|162 A|165 - A|209 }A165 - 209
3X-RAY DIFFRACTION2{ B|0 - B|161 B|166 - B|208 }B0 - 161
4X-RAY DIFFRACTION2{ B|0 - B|161 B|166 - B|208 }B166 - 208
5X-RAY DIFFRACTION3{ C|1 - C|54 C|59 - C|196 C|200 - C|209 }C1 - 54
6X-RAY DIFFRACTION3{ C|1 - C|54 C|59 - C|196 C|200 - C|209 }C59 - 196
7X-RAY DIFFRACTION3{ C|1 - C|54 C|59 - C|196 C|200 - C|209 }C200 - 209

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