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- PDB-2ixm: Structure of human PTPA -

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Basic information

Entry
Database: PDB / ID: 2ixm
TitleStructure of human PTPA
ComponentsSERINE/THREONINE-PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT B'
KeywordsHYDROLASE ACTIVATOR / PROTEIN PHOSPHATASE 2A / 2 PTPA / PPIASE
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / regulation of phosphoprotein phosphatase activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / negative regulation of phosphoprotein phosphatase activity / ATPase complex / positive regulation of phosphoprotein phosphatase activity / positive regulation of protein dephosphorylation / calcium channel complex ...protein tyrosine phosphatase activator activity / negative regulation of protein dephosphorylation / regulation of phosphoprotein phosphatase activity / protein phosphatase type 2A complex / protein phosphatase regulator activity / negative regulation of phosphoprotein phosphatase activity / ATPase complex / positive regulation of phosphoprotein phosphatase activity / positive regulation of protein dephosphorylation / calcium channel complex / mitotic spindle organization / protein phosphatase 2A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of apoptotic process / signaling receptor binding / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / 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
Serine/threonine-protein phosphatase 2A activator
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT B'


Theoretical massNumber of molelcules
Total (without water)34,7981
Polymers34,7981
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.243, 70.410, 95.534
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 2A REGULATORY SUBUNIT B' / PROTEIN PHOSPHATASE 2A ACTIVATOR / PP2A / SUBUNIT B' / PR53 ISOFORM / PHOSPHOTYROSYL PHOSPHATASE ...PROTEIN PHOSPHATASE 2A ACTIVATOR / PP2A / SUBUNIT B' / PR53 ISOFORM / PHOSPHOTYROSYL PHOSPHATASE ACTIVATOR / PTPA


Mass: 34798.031 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q15257
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 20 TO 322. THIS SEQUENCE CORRESPONDS TO AN ISOFORM OF UNIPROT ENTRY Q15257: Q15257-2

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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: 2.16 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PTPA CRYSTALS WERE GROWN USING THE HANGING DROP METHOD AT 20C. 1UL OF PROTEIN (20 MG/ML) WAS MIXED WITH 1 UL OF PRECIPITANT (23% TO 28% PEG 4000, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 7.0-8.5 ...Details: PTPA CRYSTALS WERE GROWN USING THE HANGING DROP METHOD AT 20C. 1UL OF PROTEIN (20 MG/ML) WAS MIXED WITH 1 UL OF PRECIPITANT (23% TO 28% PEG 4000, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 7.0-8.5 AND 5 MM DTT) WERE EQUILIBRATED AGAINST 0.5 ML OF PRECIPITANT. LARGE PLATE CRYSTALS APPEARED IN 2 TO 3 DAYS. FOR CRYOPROTECTION 5% MPD WAS ADDED TO THE PRECIPITANT SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9686
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.5→22 Å / Num. obs: 311889 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→56.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.123 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2690 5.1 %RANDOM
Rwork0.202 ---
obs0.203 50109 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.5→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 0 242 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222509
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.953407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0525303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77323.913115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5141512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21225
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21762
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7031.51544
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1222443
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86831106
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9244.5962
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 194
Rwork0.217 3626

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