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- PDB-1s95: Structure of serine/threonine protein phosphatase 5 -

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Basic information

Entry
Database: PDB / ID: 1s95
TitleStructure of serine/threonine protein phosphatase 5
ComponentsSerine/threonine protein phosphatase 5Serine/threonine-specific protein kinase
KeywordsHYDROLASE / protein phosphatase / PPPase / PP5 / phosphate anion / metal ion / metallophosphoesterase
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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...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 / 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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSwingle, M.R. / Honkanen, R.E. / Ciszak, E.M.
CitationJournal: 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
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
B: Serine/threonine protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,42010
Polymers75,7742
Non-polymers6468
Water8,341463
1
A: Serine/threonine protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2105
Polymers37,8871
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2105
Polymers37,8871
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-82 kcal/mol
Surface area24910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.808, 80.309, 92.189
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37887.020 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pMalc2E / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.45 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2-methyl,2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→40 Å / Num. all: 70964 / Num. obs: 70964 / % possible obs: 70 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 8.9
Reflection shellResolution: 1.47→1.59 Å / Redundancy: 1 % / % possible all: 13

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partial homology model derived from 1IT6, 1AUJ, 1G5B

1it6

1auj

1g5b


Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.112 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20933 3431 5 %RANDOM
Rwork0.16929 ---
all0.17125 70964 --
obs0.17125 70964 86.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.47 Å2
2--1.79 Å20 Å2
3----1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.039 Å0.31 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 30 463 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225404
X-RAY DIFFRACTIONr_bond_other_d0.0010.024786
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9497311
X-RAY DIFFRACTIONr_angle_other_deg0.958311221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4455646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.79924.887266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2351522
X-RAY DIFFRACTIONr_chiral_restr0.1330.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
X-RAY DIFFRACTIONr_nbd_refined0.2250.21255
X-RAY DIFFRACTIONr_nbd_other0.1950.25140
X-RAY DIFFRACTIONr_nbtor_other0.0890.23020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.243
X-RAY DIFFRACTIONr_mcbond_it1.2241.54127
X-RAY DIFFRACTIONr_mcbond_other0.3411.51320
X-RAY DIFFRACTIONr_mcangle_it1.32325255
X-RAY DIFFRACTIONr_scbond_it2.65232535
X-RAY DIFFRACTIONr_scangle_it3.5464.52056
LS refinement shellResolution: 1.6→1.68 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.354 207
Rwork0.319 4266
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)
11.90220.303-0.29870.6785-0.38952.85750.0152-0.0088-0.03820.0357-0.01410.00960.04460.005-0.0011-0.1201-0.0034-0.0112-0.1364-0.0099-0.098414.104531.936232.6582
21.6364-0.1010.22790.9721-0.30882.49090.04750.0268-0.01970.0349-0.00170.03960.0575-0.0388-0.0458-0.16420.00010.0063-0.2328-0.0175-0.10633.3071-2.392114.3794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA176 - 49910 - 333
2X-RAY DIFFRACTION2BB175 - 4999 - 333

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