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- PDB-2yga: E88G-N92L Mutant of N-Term HSP90 complexed with Geldanamycin -

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Basic information

Entry
Database: PDB / ID: 2yga
TitleE88G-N92L Mutant of N-Term HSP90 complexed with Geldanamycin
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE
Function / homology
Function and homology information


The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / 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-, 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
GELDANAMYCIN / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsRoe, S.M. / Prodromou, C. / Pearl, L.H.
CitationJournal: Faseb J. / Year: 2011
Title: Features of the Streptomyces Hygroscopicus Htpg Reveal How Partial Geldanamycin Resistance Can Arise with Mutation to the ATP Binding Pocket of a Eukaryotic Hsp90.
Authors: Millson, S.H. / Chua, C. / Roe, S.M. / Polier, S. / Solovieva, S. / Pearl, L.H. / Sim, T. / Prodromou, C. / Piper, P.W.
History
DepositionApr 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Feb 6, 2013Group: Atomic model / Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3612
Polymers24,8001
Non-polymers5611
Water73941
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules

A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7224
Polymers49,6012
Non-polymers1,1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area3890 Å2
ΔGint-29.7 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 74.340, 110.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / 82 KDA HEAT SHOCK PROTEIN / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / HSP90


Mass: 24800.393 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, RESIDUES 1-220 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Chemical ChemComp-GDM / GELDANAMYCIN / Geldanamycin


Mass: 560.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 88 TO GLY ENGINEERED RESIDUE IN CHAIN A, ASN 92 TO LEU

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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: 3.14 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 13126 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 52.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 2.37→2.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 2.37→44.233 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1176 4.9 %
Rwork0.1841 --
obs0.187 23880 99.72 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.878 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.754 Å20 Å20 Å2
2---7.754 Å20 Å2
3---15.5081 Å2
Refinement stepCycle: LAST / Resolution: 2.37→44.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 40 41 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071746
X-RAY DIFFRACTIONf_angle_d1.1292357
X-RAY DIFFRACTIONf_dihedral_angle_d15.362660
X-RAY DIFFRACTIONf_chiral_restr0.073275
X-RAY DIFFRACTIONf_plane_restr0.003300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3701-2.4780.35781420.28972846X-RAY DIFFRACTION100
2.478-2.60860.34171570.26742802X-RAY DIFFRACTION99
2.6086-2.7720.31281790.23072831X-RAY DIFFRACTION100
2.772-2.9860.24211360.19792847X-RAY DIFFRACTION100
2.986-3.28640.26771590.18672809X-RAY DIFFRACTION100
3.2864-3.76170.25451250.16382881X-RAY DIFFRACTION100
3.7617-4.73850.22511340.16252851X-RAY DIFFRACTION100
4.7385-44.24050.20371440.17592837X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.94 Å / Origin y: -31.0888 Å / Origin z: 0.9374 Å
111213212223313233
T0.2801 Å20.0094 Å20.0015 Å2-0.2131 Å20.0085 Å2--0.2055 Å2
L4.9403 °2-0.2983 °2-0.5489 °2-2.2391 °20.0485 °2--1.5286 °2
S-0.0014 Å °-0.1914 Å °-0.3447 Å °0.0491 Å °0.0046 Å °-0.2754 Å °0.0293 Å °0.0942 Å °0.0017 Å °
Refinement TLS groupSelection details: ALL

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