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- PDB-3hjc: Crystal structure of the carboxy-terminal domain of HSP90 from Le... -

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Basic information

Entry
Database: PDB / ID: 3hjc
TitleCrystal structure of the carboxy-terminal domain of HSP90 from Leishmania major, LmjF33.0312
ComponentsHeat shock protein 83-1Heat shock response
KeywordsCHAPERONE / SLEEPING SICKNESS / LEISHMANIA / HEAT SHOCK PROTEIN / STRUCTURAL GENOMICS / STRESS RESPONSE PROTEIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Stress response
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 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein 83-1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Tempel, W. / Walker, J. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. ...Wernimont, A.K. / Tempel, W. / Walker, J. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the middle and carboxy-terminal domain of HSP90 from Leishmania major, LMJF33.0312
Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / ...Authors: Wernimont, A.K. / Tempel, W. / Lin, Y.H. / Hutchinson, A. / Mackenzie, F. / Fairlamb, A. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelts, J. / Edwards, A.M. / Ferguson, M.A.J. / Hui, R. / Pizarro, J.C. / Hills, T.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1203
Polymers51,9281
Non-polymers1922
Water1,58588
1
A: Heat shock protein 83-1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)312,72218
Polymers311,5696
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area21570 Å2
ΔGint-324 kcal/mol
Surface area108550 Å2
MethodPISA
2
A: Heat shock protein 83-1
hetero molecules

A: Heat shock protein 83-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2416
Polymers103,8562
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area3350 Å2
ΔGint-92 kcal/mol
Surface area40020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.241, 169.241, 83.317
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 51928.223 Da / Num. of mol.: 1 / Fragment: UNP residues 265-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: FRIEDLIN
Gene: LmjF33.0312, LmjF33.0314, LmjF33.0316, LmjF33.0320, LmjF33.0323, LmjF33.0326, LmjF33.0333, LmjF33.0336, LmjF33.0340, LmjF33.0343, LmjF33.0346, LmjF33.0350, LmjF33.0355, LmjF33.0360, LmjF33.0365
Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRare2 / References: UniProt: Q4Q4I6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.4 M Ammonium Sulfate 0.1 M Citric Acid pH 5.5 2 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 25015 / Num. obs: 25015 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 69.776 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.128 / Χ2: 1.59 / Net I/σ(I): 27.619
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2448 / Χ2: 1.904 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å24.92 Å
Translation2.65 Å24.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USU

1usu


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.803 / SU B: 17.952 / SU ML: 0.182 / SU R Cruickshank DPI: 0.294 / SU Rfree: 0.258 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.294 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1268 5.1 %RANDOM
Rwork0.213 ---
all0.216 25064 --
obs0.216 24854 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.69 Å2 / Biso mean: 30.611 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0.87 Å20 Å2
2---1.74 Å20 Å2
3---2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 10 88 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223160
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9724252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3755390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42924.375144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8451520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212332
X-RAY DIFFRACTIONr_mcbond_it0.4931.51940
X-RAY DIFFRACTIONr_mcangle_it0.96223120
X-RAY DIFFRACTIONr_scbond_it1.5431220
X-RAY DIFFRACTIONr_scangle_it2.6184.51128
LS refinement shellResolution: 2.5→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 96 -
Rwork0.271 1623 -
all-1719 -
obs--95.08 %
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)
12.87420.0552-0.29227.52120.63511.75980.0492-0.03980.1628-0.0461-0.0008-0.1932-0.17860.1207-0.04840.08970.0062-0.01280.0861-0.00540.0193-68.40339.7167-2.8709
21.7789-0.05940.71159.87951.07052.81930.00690.15410.1535-0.42220.003-0.06610.01520.0531-0.00990.10030.04760.02850.06390.03330.025-63.524610.2699-9.2867
31.00371.67282.14333.64461.79538.33220.13320.2912-0.7820.04370.0348-2.00020.3861.5067-0.1680.68280.1450.19090.57670.07931.2627-55.3166-9.9776-20.0812
45.6039-0.98450.2898.25911.94266.0776-0.06760.6446-0.0653-1.1210.0389-0.09050.19-0.11850.02870.40550.00280.00570.2163-0.0170.0037-70.0772-6.182-26.0969
510.42583.2966-0.25961.7446-1.63453.7336-0.13580.3977-0.0835-0.26390.10690.03760.3723-0.09330.02890.44840.0541-0.05070.2118-0.03080.1206-83.7647-9.3035-25.3409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 156
2X-RAY DIFFRACTION2A157 - 254
3X-RAY DIFFRACTION3A255 - 279
4X-RAY DIFFRACTION4A280 - 371
5X-RAY DIFFRACTION5A372 - 406

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