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

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Basic information

Entry
Database: PDB / ID: 3omu
TitleCrystal Structure of the N-terminal domain of an HSP90 from Trypanosoma Brucei, Tb10.26.1080 in the presence of a thienopyrimidine derivative
ComponentsHeat shock protein 83
KeywordsCHAPERONE / hsp90 / Trypanosoma bruceii / structural genomics / drug discovery / Structural Genomics Consortium / SGC
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 / 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-, 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
Chem-IBD / Heat shock protein 83
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Sullivan, H. / Weadge, J. / Cossar, D. / Li, Y. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / 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. / Pizarro, J.C. / 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 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 1.4Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3664
Polymers52,4012
Non-polymers9652
Water1,72996
1
A: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6832
Polymers26,2001
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6832
Polymers26,2001
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.044, 60.941, 126.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein 83


Mass: 26200.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.26.1080 / Plasmid: PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)RIL / References: UniProt: Q389P1
#2: Chemical ChemComp-IBD / 2-amino-4-{2,4-dichloro-5-[2-(diethylamino)ethoxy]phenyl}-N-ethylthieno[2,3-d]pyrimidine-6-carboxamide


Mass: 482.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25Cl2N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350 0.2 M Ammonium Acetate 0.1 M Hepes pH 7.5 4 mM MgCl2 2 mM TCEP 2 mM DDU101329, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. all: 26165 / Num. obs: 25590 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.594 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.196.60.7243.0512521.29997.1
2.19-2.236.60.65712261.33296.2
2.23-2.276.50.56612621.34498
2.27-2.326.60.5212481.36196.5
2.32-2.376.50.44412431.33198
2.37-2.426.50.39412411.4196.7
2.42-2.486.50.30312561.497
2.48-2.556.50.26712441.42596.7
2.55-2.626.50.23412321.43296.1
2.62-2.716.50.20412591.50396.5
2.71-2.816.60.16712421.5196.4
2.81-2.926.60.13812621.52496.9
2.92-3.056.70.10613021.63598.4
3.05-3.216.90.08412801.7298.8
3.21-3.417.10.06812921.79299.1
3.41-3.687.10.05413081.93999.5
3.68-4.0470.04313291.84399.3
4.04-4.636.90.03813221.98999.5
4.63-5.836.80.03713491.97499.9
5.83-356.20.03114411.86199

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.16 Å
Translation2.5 Å28.16 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O6O

3o6o


Resolution: 2.15→28.16 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2619 / WRfactor Rwork: 0.2147 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8281 / SU B: 12.683 / SU ML: 0.162 / SU R Cruickshank DPI: 0.2737 / SU Rfree: 0.2235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1298 5.1 %RANDOM
Rwork0.2239 ---
obs0.2264 25447 97.27 %-
all-26160 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.31 Å2 / Biso mean: 41.707 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2--1.2 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 62 96 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223286
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9774455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38824.83147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40415554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9391519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022481
X-RAY DIFFRACTIONr_mcbond_it0.371.52055
X-RAY DIFFRACTIONr_mcangle_it0.71223297
X-RAY DIFFRACTIONr_scbond_it1.20831231
X-RAY DIFFRACTIONr_scangle_it1.9814.51158
LS refinement shellResolution: 2.147→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 95 -
Rwork0.282 1675 -
all-1770 -
obs-1252 93.6 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.39950.32610.44890.66360.09471.8890.03540.00750.0234-0.0275-0.06620.061-0.0333-0.12660.03080.2887-0.0132-0.0090.2960.01770.31623.364-2.57395.9843
22.60020.50511.57632.01563.57846.59070.1121-0.6638-0.0301-0.0728-0.11490.0808-0.0848-0.39510.00280.2893-0.08450.06550.49770.04760.343-5.8678-5.734621.3703
33.2222-0.1337-0.10120.55690.59610.69510.1538-0.19370.5081-0.0258-0.13740.0758-0.0367-0.107-0.01650.30780.01360.00420.3255-0.01190.3526-0.58853.10259.263
42.3914-0.1949-0.30481.62560.43661.41630.06740.08190.1181-0.0781-0.08520.0811-0.0503-0.08790.01780.30080.00430.00220.26190.01730.3162.7236-1.24194.7121
51.57351.17080.12251.65970.03910.94360.0916-0.1158-0.1731-0.0184-0.03980.11720.1415-0.3342-0.05180.2771-0.0306-0.02090.3531-0.00280.346-5.9435-9.24186.9569
64.88490.76681.53896.46674.84324.24980.3543-0.7546-0.45520.2171-0.0102-0.32140.2662-0.1542-0.3440.3573-0.1133-0.03110.32810.190.31583.8076-15.201619.1382
74.4512.9184-2.27381.9402-1.7154.587-0.2150.18120.2358-0.21210.17020.13260.217-0.25430.04480.3915-0.07130.0310.26120.02840.418721.087418.84359.2664
84.2921-2.92281.83752.2578-0.54434.9434-0.4226-0.3760.53640.35960.014-0.1918-0.18410.15620.40870.296-0.03820.060.7801-0.15720.381111.17716.543126.1013
93.412-0.72540.25047.6244.07722.85820.0364-0.4444-1.00690.2522-0.1440.07820.1968-0.18430.10760.3332-0.05840.08760.31330.13030.573117.962-6.633317.1547
1010.0117-4.73742.64279.53451.32043.9015-0.6874-2.8883-1.30642.35070.9278-0.87951.0319-0.2813-0.24041.27180.1146-0.24691.05720.65310.653626.65850.369727.7291
115.2969-0.45270.33791.41020.5820.47590.0146-0.11340.3599-0.1458-0.03360.0542-0.0543-0.13210.01910.3590.00140.03010.29040.01840.316514.583710.795515.1495
126.6186-1.1933-1.33843.06860.67350.58460.0153-0.29850.2692-0.0580.0675-0.1679-0.1102-0.0131-0.08280.34670.0062-0.00950.32090.00110.261422.32139.917317.5235
133.8459-0.2025-0.30013.0290.10410.9567-0.0652-0.60790.0985-0.10450.0262-0.42170.05550.17760.0390.3158-0.0140.00150.3397-0.00920.312428.83288.762619.563
147.72081.73190.878913.4497.14133.8114-0.4-1.8869-0.10210.10390.4422-0.11080.10580.1759-0.04220.44060.05730.09490.80530.04980.04716.71945.935534.4959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 46
2X-RAY DIFFRACTION2A47 - 73
3X-RAY DIFFRACTION3A74 - 103
4X-RAY DIFFRACTION4A104 - 152
5X-RAY DIFFRACTION5A153 - 188
6X-RAY DIFFRACTION6A189 - 208
7X-RAY DIFFRACTION7B2 - 15
8X-RAY DIFFRACTION8B16 - 33
9X-RAY DIFFRACTION9B34 - 53
10X-RAY DIFFRACTION10B54 - 73
11X-RAY DIFFRACTION11B74 - 117
12X-RAY DIFFRACTION12B118 - 150
13X-RAY DIFFRACTION13B154 - 177
14X-RAY DIFFRACTION14B178 - 207

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