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- PDB-2ixp: Crystal structure of the Pp2A phosphatase activator Ypa1 PTPA1 in... -

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Basic information

Entry
Database: PDB / ID: 2ixp
TitleCrystal structure of the Pp2A phosphatase activator Ypa1 PTPA1 in complex with model substrate
Components
  • SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
  • SIN-ALA-ALA-PRO-LYS-NIT
KeywordsISOMERASE/ISOMERASE INHIBITOR / PP2A PHOSPHATASE ACTIVATOR PROLYL ISOMERASE PTPA / PROLYL CONTAINING PEPTIDE SUBSTRATE ANALOG / NUCLEAR PROTEIN / ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / TOR signaling / mitotic spindle organization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / autophagy / G1/S transition of mitotic cell cycle / DNA repair ...protein tyrosine phosphatase activator activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / TOR signaling / mitotic spindle organization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / autophagy / G1/S transition of mitotic cell cycle / DNA repair / chromatin / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Phosphotyrosyl phosphate activator, C-terminal lid domain / Phosphotyrosyl phosphatase activator, PTPA / PTPA superfamily / Phosphotyrosyl phosphatase activator, C-terminal lid domain / Phosphotyrosyl phosphate activator (PTPA) protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
N-(3-carboxypropanoyl)-L-alanyl-L-alanyl-L-prolyl-6-ammonio-N-(4-nitrophenyl)-L-norleucinamide / Serine/threonine-protein phosphatase 2A activator 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLeulliot, N. / Vicentini, G. / Jordens, J. / Quevillon-Cheruel, S. / Schiltz, M. / Barford, D. / Van Tilbeurgh, H. / Goris, J.
CitationJournal: Mol. Cell / Year: 2006
Title: Crystal structure of the PP2A phosphatase activator: implications for its PP2A-specific PPIase activity.
Authors: Leulliot, N. / Vicentini, G. / Jordens, J. / Quevillon-Cheruel, S. / Schiltz, M. / Barford, D. / van Tilbeurgh, H. / Goris, J.
History
DepositionJul 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 28, 2016Group: Database references / Other / Source and taxonomy
Revision 2.0Nov 28, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct / struct_conn
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _struct.title
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
B: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
C: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
D: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
F: SIN-ALA-ALA-PRO-LYS-NIT
G: SIN-ALA-ALA-PRO-LYS-NIT
H: SIN-ALA-ALA-PRO-LYS-NIT
I: SIN-ALA-ALA-PRO-LYS-NIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,73814
Polymers152,2828
Non-polymers4556
Water00
1
A: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
C: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
F: SIN-ALA-ALA-PRO-LYS-NIT
G: SIN-ALA-ALA-PRO-LYS-NIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3697
Polymers76,1414
Non-polymers2283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-31.7 kcal/mol
Surface area31260 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
D: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1
H: SIN-ALA-ALA-PRO-LYS-NIT
I: SIN-ALA-ALA-PRO-LYS-NIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3697
Polymers76,1414
Non-polymers2283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-22.6 kcal/mol
Surface area31320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)86.886, 86.886, 410.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
SERINE/THREONINE-PROTEIN PHOSPHATASE 2A ACTIVATOR 1 / PTPA1 / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PTPA-1 / PPIASE PTPA-1 / ROTAMASE PTPA-1 / ...PTPA1 / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PTPA-1 / PPIASE PTPA-1 / ROTAMASE PTPA-1 / PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR 1


Mass: 37463.945 Da / Num. of mol.: 4 / Fragment: 1-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P40454*PLUS
#2: Protein/peptide
SIN-ALA-ALA-PRO-LYS-NIT


Type: Peptide-like / Class: Inhibitor / Mass: 606.647 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
References: N-(3-carboxypropanoyl)-L-alanyl-L-alanyl-L-prolyl-6-ammonio-N-(4-nitrophenyl)-L-norleucinamide
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Compound detailsTHE PEPTIDE IS A PROLINE CONTAINING SUBTSTRATE PEPTIDE ANALOG
Sequence detailsRESIDUES 1-317 AND C-TERMINAL HIS TAG

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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: 3.07 Å3/Da / Density % sol: 59.68 %
Crystal growpH: 6.5
Details: 1.8MM PEPTIDE, 1M AMMONIUM SULFATE, 3% GLYCEROL, 0.1M ADA PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 42938 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IXO

2ixo


Resolution: 2.8→29.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / SU B: 40.408 / SU ML: 0.362 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.302 2158 5 %RANDOM
Rwork0.229 ---
obs0.233 40651 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å21.5 Å20 Å2
2--3.01 Å20 Å2
3----4.51 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10372 0 22 0 10394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02210720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4661.95314564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.04551258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37523.21486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.401151726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2451552
X-RAY DIFFRACTIONr_chiral_restr0.1740.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.25792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3430.27237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2426
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3541.56515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.215210276
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.72934886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1954.54288
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: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.413 146
Rwork0.319 2963
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8353-0.5808-0.45961.719-0.23743.14370.07520.1545-0.024-0.2282-0.00880.159-0.2569-0.497-0.0663-0.1076-0.08990.01570.056-0.0504-0.092-23.437-12.48-0.271
21.6175-0.38630.12382.5444-0.47934.9432-0.0648-0.0109-0.21310.01320.0636-0.05740.16310.36380.0012-0.2040.03260.03250.0620.0341-0.0933-64.215-13.8927.196
31.9105-0.2723-0.26552.25950.24814.59370.0269-0.1176-0.149-0.0942-0.0147-0.16160.3798-0.0474-0.01230.0106-0.09380.0427-0.19370.0026-0.08180.697-26.564-26.577
41.43430.6097-0.4333.6419-0.32323.2273-0.0424-0.03990.16710.26710.1345-0.0803-0.50740.0776-0.0921-0.0649-0.1258-0.03150.02410.0586-0.0893-64.41314.0990.801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 317
2X-RAY DIFFRACTION2B2 - 317
3X-RAY DIFFRACTION3C2 - 317
4X-RAY DIFFRACTION4D2 - 317

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