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- PDB-3e7b: Crystal Structure of Protein Phosphatase-1 Bound to the natural t... -

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Basic information

Entry
Database: PDB / ID: 3e7b
TitleCrystal Structure of Protein Phosphatase-1 Bound to the natural toxin inhibitor Tautomycin
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / protein phosphatase 1 / tautomycin / molecular toxin / Carbohydrate metabolism / Cell cycle / Cell division / Glycogen metabolism / Iron / Manganese / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Chem-E7B / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKelker, M.S. / Page, R. / Peti, W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of protein phosphatase-1 bound to nodularin-R and tautomycin: a novel scaffold for structure-based drug design of serine/threonine phosphatase inhibitors
Authors: Kelker, M.S. / Page, R. / Peti, W.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / 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 / _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 PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,51717
Polymers68,3242
Non-polymers2,19215
Water8,773487
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,37611
Polymers34,1621
Non-polymers1,21310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1416
Polymers34,1621
Non-polymers9795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.760, 78.519, 130.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Plasmid: in-house derived / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P62136, protein-serine/threonine phosphatase

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Non-polymers , 7 types, 502 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-E7B / (2Z)-2-[(1R)-3-{[(1R,2S,3R,6S,7S,10R)-10-{(2S,3S,6R,8S,9R)-3,9-dimethyl-8-[(3S)-3-methyl-4-oxopentyl]-1,7-dioxaspiro[5.5]undec-2-yl}-3,7-dihydroxy-2-methoxy-6-methyl-1-(1-methylethyl)-5-oxoundecyl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid


Mass: 784.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H68O14
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 298 K / pH: 8
Details: 0.1M Tris, 30% PEG 6K, 1M Lithium Sulfate, pH 8.0, under paraffin oil, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 18, 2008 / Details: OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR.
RadiationMonochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 74099 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rsym value: 0.046
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.511 / % possible all: 93.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.51 Å
Translation2.5 Å27.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E7A

3e7a


Resolution: 1.7→19.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.347 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17521 3750 5 %RANDOM
Rwork0.15294 ---
obs0.15408 70860 99.22 %-
all-74713 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.298 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 140 487 5257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225006
X-RAY DIFFRACTIONr_bond_other_d0.0010.023414
X-RAY DIFFRACTIONr_angle_refined_deg1.5712.0016812
X-RAY DIFFRACTIONr_angle_other_deg1.0963.0028223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93423.81231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31215827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8971532
X-RAY DIFFRACTIONr_chiral_restr0.1370.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_nbd_refined0.2020.21049
X-RAY DIFFRACTIONr_nbd_other0.2020.23637
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22450
X-RAY DIFFRACTIONr_nbtor_other0.090.22597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.39132988
X-RAY DIFFRACTIONr_mcbond_other0.40931215
X-RAY DIFFRACTIONr_mcangle_it2.28454823
X-RAY DIFFRACTIONr_scbond_it3.6582069
X-RAY DIFFRACTIONr_scangle_it5.036111966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 249 -
Rwork0.244 4783 -
obs--91.84 %
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)
14.37951.07440.20895.24791.28454.1012-0.139-0.13680.0368-0.04490.09920.0036-0.0796-0.24290.0398-0.09930.00660.0114-0.0457-0.02330.0096-12.03827.4726.61
20.9473-0.0930.61570.5173-0.08891.22610.03390.1442-0.0084-0.0517-0.02120.00960.06480.147-0.0126-0.0780.00360.0024-0.0643-0.00590.0016-2.17823.404-7.128
31.6104-0.16070.44511.40170.1791.70770.00840.57630.1351-0.3149-0.0977-0.1245-0.05360.50590.0893-0.0026-0.01240.03480.19150.0608-0.05123.73529.568-25.199
40.92870.24650.85483.11041.21143.0678-0.21380.28290.2785-0.1821-0.04110.0281-0.27570.38580.2549-0.0273-0.0483-0.0362-0.00270.07190.0086-3.88536.678-18.941
51.59540.59241.75052.36110.97552.9011-0.08020.1080.0923-0.0789-0.0319-0.0609-0.25710.01520.1121-0.0183-0.0203-0.0358-0.07450.03530.0142-11.40337.168-16.495
61.4841-1.62971.3673.891-0.99183.96280.08250.13230.022-0.03620.0141-0.18270.33620.2472-0.0966-0.03060.022-0.0054-0.09950.0136-0.0093-27.46743.708-46.027
71.4227-0.47510.89630.7642-0.63981.7754-0.1164-0.3593-0.0040.12480.22130.0534-0.1208-0.3944-0.1049-0.0340.05360.0088-0.00860.0392-0.0308-34.50948.41-30.457
81.6419-0.80610.05762.5862-0.44541.5146-0.2412-0.64310.12660.54390.23410.0285-0.445-0.37670.00710.17550.1837-0.01280.1893-0.031-0.086-30.63554.829-12.879
91.74870.2180.45571.4358-1.51631.8756-0.2035-0.48340.0860.32750.1536-0.1877-0.3697-0.08340.050.05670.0894-0.05070.02590.0043-0.0497-21.69349.468-17.253
102.55540.09560.3612.663-2.3462.9689-0.0926-0.17420.11810.15630.1416-0.0543-0.18-0.2045-0.049-0.02460.0233-0.0345-0.08370.0232-0.022-18.51443.798-22.046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 25
2X-RAY DIFFRACTION2A26 - 195
3X-RAY DIFFRACTION3A196 - 258
4X-RAY DIFFRACTION4A259 - 273
5X-RAY DIFFRACTION5A274 - 299
6X-RAY DIFFRACTION6B7 - 32
7X-RAY DIFFRACTION7B33 - 193
8X-RAY DIFFRACTION8B194 - 257
9X-RAY DIFFRACTION9B258 - 272
10X-RAY DIFFRACTION10B273 - 299

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