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- PDB-1ejf: CRYSTAL STRUCTURE OF THE HUMAN CO-CHAPERONE P23 -

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Basic information

Entry
Database: PDB / ID: 1ejf
TitleCRYSTAL STRUCTURE OF THE HUMAN CO-CHAPERONE P23
ComponentsProstaglandin E synthase 3
KeywordsCHAPERONE / Co-Chaperone / Beta-Sandwich
Function / homology
Function and homology information


lung saccule development / prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / nuclear receptor-mediated glucocorticoid signaling pathway / Aryl hydrocarbon receptor signalling / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / telomerase holoenzyme complex / glycogen biosynthetic process ...lung saccule development / prostaglandin-E synthase / prostaglandin-E synthase activity / telomerase activity / nuclear receptor-mediated glucocorticoid signaling pathway / Aryl hydrocarbon receptor signalling / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / telomerase holoenzyme complex / glycogen biosynthetic process / protein folding chaperone complex / prostaglandin biosynthetic process / skin development / telomerase holoenzyme complex assembly / : / chaperone cofactor-dependent protein refolding / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / DNA polymerase binding / positive regulation of phosphorylation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / telomere maintenance / ESR-mediated signaling / Hsp90 protein binding / unfolded protein binding / protein folding / protein-folding chaperone binding / fibroblast proliferation / Estrogen-dependent gene expression / Potential therapeutics for SARS / chromosome, telomeric region / protein stabilization / signal transduction / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Prostaglandin E synthase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsWeaver, A.J. / Sullivan, W.P. / Felts, S.J. / Owen, B.A.L. / Toft, D.O.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure and activity of human p23, a heat shock protein 90 co-chaperone.
Authors: Weaver, A.J. / Sullivan, W.P. / Felts, S.J. / Owen, B.A. / Toft, D.O.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.4Oct 28, 2020Group: Derived calculations / Structure summary / Category: entity / entity_name_com / struct_site
Item: _entity.pdbx_description / _struct_site.pdbx_auth_asym_id ..._entity.pdbx_description / _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

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Assembly

Deposited unit
A: Prostaglandin E synthase 3
B: Prostaglandin E synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0735
Polymers29,7852
Non-polymers2883
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-24 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.802, 61.802, 162.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Prostaglandin E synthase 3 / p23 / Hsp90 co-chaperone


Mass: 14892.471 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: DE3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15185
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulfate, bicine, tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9-2.1 Mammonium sulfate1reservoir
20.1 MBicine1reservoirpH9.0
320 mg/mlprotein1drop
410 mMTris-HCl1droppH7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9159
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.49→100 Å / Num. all: 11727 / Num. obs: 11651 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.7
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.074 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 11743 / Num. measured all: 97860 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98.8 % / Num. unique obs: 1651 / Num. measured obs: 11297 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.49→100 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 554 4.8 %RANDOM
Rwork0.236 ---
all0.238 11727 --
obs0.238 11651 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.8 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.49→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 15 58 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.002
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.39
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shellResolution: 2.49→2.65 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 94 5 %
Rwork0.3 1800 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.39
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scangle_it4.892.5
LS refinement shell
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.3

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