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- PDB-1a17: TETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5 -

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Basic information

Entry
Database: PDB / ID: 1a17
TitleTETRATRICOPEPTIDE REPEATS OF PROTEIN PHOSPHATASE 5
ComponentsSERINE/THREONINE PROTEIN PHOSPHATASE 5Serine/threonine-specific protein kinase
KeywordsHYDROLASE / PHOSPHATASE / PROTEIN-PROTEIN INTERACTIONS / TPR / SUPER-HELIX
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 / ESR-mediated signaling / protein dephosphorylation / ADP binding / response to lead ion / Hsp90 protein binding / tau protein binding / Negative regulation of MAPK pathway / double-strand break repair / MAPK cascade / 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 / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase 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 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type ...PPP domain / PP5, C-terminal metallophosphatase 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 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.45 Å
AuthorsDas, A.K. / Cohen, P.T.W. / Barford, D.
CitationJournal: EMBO J. / Year: 1998
Title: The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions.
Authors: Das, A.K. / Cohen, P.W. / Barford, D.
History
DepositionDec 23, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2533
Polymers19,0611
Non-polymers1922
Water1,40578
1
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,01112
Polymers76,2424
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
MethodPQS
2
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules

A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5056
Polymers38,1212
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
Buried area5090 Å2
ΔGint-87 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.060, 90.060, 104.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE 5 / Serine/threonine-specific protein kinase / TETRATRICOPEPTIDE / TRP


Mass: 19060.549 Da / Num. of mol.: 1 / Fragment: PROTEIN INTERACTING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BRAIN / Gene: PPP5 / Plasmid: PT7.7 / Gene (production host): PPP5 / Production host: Escherichia coli (E. coli) / Strain (production host): PT7.7 / Tissue (production host): BRAIN
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5
Details: 1.8 M AMMONIUM SULFATE, 4% MPD, 100 MM HEPES PH 7.5, 2 MM DTT
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium salfate1reservoir
24 %(v/v)MPD1reservoir
3100 mMHEPES1reservoir
42 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. obs: 7832 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 24.4
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 3 / Rsym value: 0.133 / % possible all: 97.6

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.45→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1045 13.4 %RANDOM
Rwork0.201 ---
obs0.201 7796 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 10 78 1369
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH.WATER
X-RAY DIFFRACTION3PARAM.SULPHATETOP.SULPHATE
X-RAY DIFFRACTION4PARAM.SULPHATETOP.SULPHATE
Software
*PLUS
Name: X-PLOR / Version: 3.82 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.754

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