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

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Basic information

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


eNOS activation / VEGFR2 mediated vascular permeability / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 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 ...eNOS activation / VEGFR2 mediated vascular permeability / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 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 / protein-containing complex / ATP hydrolysis activity / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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
MACBECIN / Endoplasmin, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å
AuthorsWernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / MacKenzie, F. / Senisterra, G. / Vedadi, M. / Cossar, D. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / MacKenzie, F. / Senisterra, G. / Vedadi, M. / Cossar, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizzaro, 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 Macbecin
Authors: Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / MacKenzie, F. / Senisterra, G. / Vedadi, M. / Cossar, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. ...Authors: Wernimont, A.K. / Tempel, W. / Hutchinson, A. / Weadge, J. / MacKenzie, F. / Senisterra, G. / Vedadi, M. / Cossar, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Pizzaro, 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 1.3Sep 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: Endoplasmin homolog
B: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5367
Polymers64,1312
Non-polymers1,4065
Water00
1
A: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7203
Polymers32,0651
Non-polymers6552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8164
Polymers32,0651
Non-polymers7513
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)65,5367
Polymers64,1312
Non-polymers1,4065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1790 Å2
ΔGint-12 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.880, 96.880, 159.698
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): BL21DE3 / References: UniProt: Q8I0V4
#2: Chemical ChemComp-BC2 / MACBECIN


Mass: 558.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42N2O8 / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
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 Mecbecin 4 mM MgCl2 2 mM TCEP ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.81→40 Å / Num. all: 19287 / Num. obs: 19268 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 75.9 Å2 / Rmerge(I) obs: 0.139 / Χ2: 1.909 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.81-2.915.70.991218681.68799.4
2.91-3.037.10.8113.3318881.696100
3.03-3.167.90.6234.6718771.72100
3.16-3.338.10.47218971.864100
3.33-3.548.10.28418901.949100
3.54-3.818.10.18319212.009100
3.81-4.280.12719082.066100
4.2-4.87.90.09219372.367100
4.8-6.057.90.09319751.967100
6.05-407.30.04221071.652100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PEH

3peh


Resolution: 2.81→39.92 Å / Cor.coef. Fo:Fc: 0.9339 / Cor.coef. Fo:Fc free: 0.9069 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 974 5.11 %RANDOM
Rwork0.2394 ---
all0.2414 19236 --
obs0.2414 19044 99 %-
Displacement parametersBiso max: 152.61 Å2 / Biso mean: 57.3994 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.0799 Å20 Å20 Å2
2---1.0799 Å20 Å2
3---2.1599 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.81→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 95 0 4111
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d14482
X-RAY DIFFRACTIONt_trig_c_planes1132
X-RAY DIFFRACTIONt_gen_planes5905
X-RAY DIFFRACTIONt_it408420
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5875
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_contact46884
X-RAY DIFFRACTIONt_bond_d416620.009
X-RAY DIFFRACTIONt_angle_deg564421.07
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion18.1
LS refinement shellResolution: 2.808→2.881 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3028 70 5.17 %
Rwork0.2711 2552 -
all0.2727 2691 -
obs-1281 -

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