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- PDB-3peh: Crystal Structure of the N-terminal domain of an HSP90 from Plasm... -

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Basic information

Entry
Database: PDB / ID: 3peh
TitleCrystal Structure of the N-terminal domain of an HSP90 from Plasmodium Falciparum, PFL1070c in the presence of a thienopyrimidine derivative
ComponentsEndoplasmin homolog
KeywordsCHAPERONE / Structural Genomics / Structural Genomics Consortium / SGC / heat shock protein / ATP binding
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / response to heat / protein stabilization / perinuclear region of cytoplasm / endoplasmic reticulum ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / response to heat / protein stabilization / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol
Similarity search - Function
Alpha-Beta Plaits - #2140 / 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 ...Alpha-Beta Plaits - #2140 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IBD / Endoplasmin, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsWernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / Cossar, D. / MacKenzie, F. / Vedadi, M. / Senisterra, G. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / Cossar, D. / MacKenzie, F. / Vedadi, M. / Senisterra, G. / 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: To be Published
Title: Crystal Structure of the N-terminal domain of an HSP90 from Plasmodium Falciparum, PFL1070c in the presence of a thienopyrimidine derivative
Authors: Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / Cossar, D. / MacKenzie, F. / Vedadi, M. / Senisterra, G. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Wyatt, ...Authors: Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / Cossar, D. / MacKenzie, F. / Vedadi, M. / Senisterra, G. / 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.
History
DepositionOct 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
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: Endoplasmin homolog
B: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2886
Polymers64,1312
Non-polymers1,1574
Water00
1
A: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6443
Polymers32,0651
Non-polymers5782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6443
Polymers32,0651
Non-polymers5782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Endoplasmin homolog
hetero molecules

B: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2886
Polymers64,1312
Non-polymers1,1574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.927, 91.927, 162.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Endoplasmin homolog


Mass: 32065.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFL1070c / Plasmid: pet15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8I0V4
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 % PEG 5k MME 0.2 M Ammonium sulfate 0.1 M MES pH 6.5 1 mM DDU compound 4 mM MgCl2 2 mM TCEP glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→35 Å / Num. all: 18810 / Num. obs: 18792 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 73.4 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.707 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.75-2.89.60.9392.959181.349100
2.8-2.859.70.7653.629141.31999.9
2.85-2.99.70.6494.299031.243100
2.9-2.969.70.5739391.233100
2.96-3.039.80.4289111.249100
3.03-3.19.90.3869091.286100
3.1-3.179.90.3189271.311100
3.17-3.269.80.2789331.30999.9
3.26-3.369.90.2179141.331100
3.36-3.469.70.1899241.601100
3.46-3.599.80.1299341.428100
3.59-3.739.60.1399272.074100
3.73-3.99.70.1019311.933100
3.9-4.119.70.0799371.81399.9
4.11-4.369.60.0679531.906100
4.36-4.79.40.069342.257100
4.7-5.179.30.0659582.497100
5.17-5.929.20.0739732.426100
5.92-7.4490.0569882.208100
7.44-3580.04110652.46799.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.8.0refinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1zw9

1zw9


Resolution: 2.75→24.33 Å / Cor.coef. Fo:Fc: 0.9446 / Cor.coef. Fo:Fc free: 0.9403 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 969 5.18 %RANDOM
Rwork0.2215 ---
all0.2237 18834 --
obs0.2237 18705 99.31 %-
Displacement parametersBiso max: 144.05 Å2 / Biso mean: 63.6199 Å2 / Biso min: 33.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.1721 Å20 Å20 Å2
2---0.1721 Å20 Å2
3---0.3442 Å2
Refine analyzeLuzzati coordinate error obs: 0.361 Å
Refinement stepCycle: LAST / Resolution: 2.75→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 72 0 4012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.15
X-RAY DIFFRACTIONo_bond_d0.01
LS refinement shellResolution: 2.75→2.823 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2582 79 5.51 %
Rwork0.2367 2712 -
all0.238 2870 -
obs-1220 -

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