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- PDB-5hpe: Phosphatase domain of PP5 bound to a phosphomimetic Cdc37 substra... -

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Basic information

Entry
Database: PDB / ID: 5hpe
TitlePhosphatase domain of PP5 bound to a phosphomimetic Cdc37 substrate peptide
ComponentsSerine/threonine-protein phosphatase 5,Hsp90 co-chaperone Cdc37
KeywordsHYDROLASE / Phosphatase domain / enzyme / substrate / phosphorylation
Function / homology
Function and homology information


response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity ...response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / ESR-mediated signaling / response to lead ion / Hsp90 protein binding / tau protein binding / ADP binding / Negative regulation of MAPK pathway / MAPK cascade / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / protein kinase binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases ...PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 4-Layer Sandwich / Tetratricopeptide-like helical domain superfamily / Alpha Beta
Similarity search - Domain/homology
: / COBALT HEXAMMINE(III) / Hsp90 co-chaperone Cdc37 / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsOberoi, J. / Mariotti, L. / Vaughan, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural and functional basis of protein phosphatase 5 substrate specificity.
Authors: Oberoi, J. / Dunn, D.M. / Woodford, M.R. / Mariotti, L. / Schulman, J. / Bourboulia, D. / Mollapour, M. / Vaughan, C.K.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 5,Hsp90 co-chaperone Cdc37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2015
Polymers39,7691
Non-polymers4324
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-12 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.314, 65.164, 132.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein phosphatase 5,Hsp90 co-chaperone Cdc37 / PP5 / Protein phosphatase T / PPT


Mass: 39768.797 Da / Num. of mol.: 1 / Mutation: S13E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5, CDC37 / Production host: Escherichia coli (E. coli)
References: UniProt: P53041, UniProt: K7EJ06, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 18% PEG, 8% ethylene glycol, 0.1M Hepes pH 7.5, 20mM hexamine cobolt chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.27→46.39 Å / Num. obs: 16821 / % possible obs: 92 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 9.5
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.1.29data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S95

1s95


Resolution: 2.27→46.39 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1681 10 %
Rwork0.1684 --
obs0.1753 16805 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 16 105 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172704
X-RAY DIFFRACTIONf_angle_d1.6323673
X-RAY DIFFRACTIONf_dihedral_angle_d15.548997
X-RAY DIFFRACTIONf_chiral_restr0.067386
X-RAY DIFFRACTIONf_plane_restr0.008477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2671-2.33380.25391250.19381127X-RAY DIFFRACTION87
2.3338-2.40920.31091410.19751267X-RAY DIFFRACTION98
2.4092-2.49530.23381410.18091273X-RAY DIFFRACTION97
2.4953-2.59510.28691400.17721257X-RAY DIFFRACTION97
2.5951-2.71320.28061390.18671243X-RAY DIFFRACTION96
2.7132-2.85630.28071410.18821272X-RAY DIFFRACTION97
2.8563-3.03520.25011430.19211285X-RAY DIFFRACTION97
3.0352-3.26950.28831410.19121275X-RAY DIFFRACTION96
3.2695-3.59840.2431400.16031256X-RAY DIFFRACTION96
3.5984-4.11880.19081420.15261279X-RAY DIFFRACTION95
4.1188-5.18820.15321420.11381279X-RAY DIFFRACTION94
5.1882-46.40060.20971460.16921311X-RAY DIFFRACTION91

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