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- PDB-3h69: Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) w... -

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Basic information

Entry
Database: PDB / ID: 3h69
TitleCatalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms complexed with endothall
ComponentsSerine/threonine-protein phosphatase 5
KeywordsHYDROLASE / metalloenzyme / phosphatase / inhibitors / drug design / Cytoplasm / Iron / Manganese / Metal-binding / Nucleus / Protein phosphatase / TPR repeat
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 / 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 / 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
Chem-ENL / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Talluri, E.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structural basis of serine/threonine phosphatase inhibition by the archetypal small molecules cantharidin and norcantharidin
Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Talluri, E.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 5
D: Serine/threonine-protein phosphatase 5
A: (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
D: (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5368
Polymers71,9022
Non-polymers6346
Water6,143341
1
A: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2684
Polymers35,9511
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2684
Polymers35,9511
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.535, 41.778, 105.483
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein phosphatase 5 / PP5c / PP5 / Protein phosphatase T / PP-T / PPT


Mass: 35950.797 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 176-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pDEST30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIPL
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ENL / (1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid / Endothall / Endothall


Mass: 186.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 39575 / Num. obs: 39575 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5696 / Rsym value: 0.358 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S95

1s95


Resolution: 2.1→38.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.899 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.216 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22703 3585 9.1 %RANDOM
Rwork0.16166 ---
all0.16767 35988 --
obs0.16767 35988 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å22.86 Å2
2---1.86 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 36 341 5433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0225218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2991.9627064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85424.688256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41115894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1951522
X-RAY DIFFRACTIONr_chiral_restr0.1520.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214010
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_it1.2711.53132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18525064
X-RAY DIFFRACTIONr_scbond_it3.91132086
X-RAY DIFFRACTIONr_scangle_it6.0744.52000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 252 -
Rwork0.198 2599 -
obs--100 %

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