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- PDB-4zx2: Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicycl... -

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Basic information

Entry
Database: PDB / ID: 4zx2
TitleCo-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
ComponentsSerine/threonine-protein phosphatase 5
KeywordsHydrolase/Hydrolase Inhibitor / Protein phosphatase 5 / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


response to arachidonate / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / protein folding chaperone complex / response to morphine / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity ...response to arachidonate / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / protein folding chaperone complex / response to morphine / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / ESR-mediated signaling / Hsp90 protein binding / response to lead ion / tau protein binding / ADP binding / Negative regulation of MAPK pathway / MAPK cascade / double-strand break repair / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / 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 ...PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / 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 / 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
Chem-4TE / : / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsChattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wierzbicki, A. / Honkanen, R.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)5U54MH084512 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1RO3MH05702 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS071553 United States
Citation
Journal: Biochem. Pharmacol. / Year: 2016
Title: Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C.
Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / ...Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / Dunham, W.H. / Gingras, A.C. / Banerjee, S. / Forbes, D. / Wierzbicki, A. / Honkanen, R.E.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5.
Authors: Swingle, M.R. / Honkanen, R.E. / Ciszak, E.M.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4336
Polymers37,8871
Non-polymers5465
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.600, 90.831, 94.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein phosphatase 5 / PP5 / Protein phosphatase T / PPT


Mass: 37887.020 Da / Num. of mol.: 1 / Fragment: UNP residues 169-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pMal2cE / Production host: Escherichia coli (E. coli)
References: UniProt: P53041, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-4TE / (1S,2R,3S,4R,5S)-5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid


Mass: 200.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O5
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% MPD, 6% PEG, 10 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.19→94.83 Å / Num. obs: 107757 / % possible obs: 94.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.19→1.25 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.9 / % possible all: 72.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S95

1s95


Resolution: 1.23→40.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.518 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.175 4984 5 %RANDOM
Rwork0.16277 ---
obs0.16339 95453 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.23→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 32 344 2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9743842
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46324.963135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1281511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212165
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 333 -
Rwork0.244 6121 -
obs--90.05 %

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