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- PDB-3e7a: Crystal Structure of Protein Phosphatase-1 Bound to the natural t... -

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Basic information

Entry
Database: PDB / ID: 3e7a
TitleCrystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R
Components
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
  • nodularin R
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Carbohydrate metabolism / Cell cycle / Cell division / Glycogen metabolism / Hydrolase / Iron / Manganese / Metal-binding / Phosphoprotein / Protein phosphatase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / 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 / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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
NODULARIN-R / AZIDE ION / IODIDE ION / : / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Nodularia spumigena (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 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 / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Apr 10, 2013Group: Derived calculations
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.5Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
C: nodularin R
D: nodularin R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,41930
Polymers70,0124
Non-polymers2,40626
Water12,286682
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: nodularin R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20315
Polymers35,0062
Non-polymers1,19713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-51 kcal/mol
Surface area11880 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: nodularin R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,21615
Polymers35,0062
Non-polymers1,21013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.354, 77.274, 132.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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
#2: Protein/peptide nodularin R / Nodularin


Type: Oligopeptide / Class: Toxin / Mass: 843.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Nodularia spumigena (bacteria) / References: NOR: NOR00279, NODULARIN-R

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Non-polymers , 6 types, 708 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 20% PEG 3350 and 0.2 M NaI, pH 7.0, under parafin oil, temperature 298K, Microbatch

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 28, 2008 / Details: Oxford Danfysik toroidal focusing mirror.
RadiationMonochromator: Monochromator: 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: 1.63→50 Å / Num. all: 83995 / Num. obs: 83444 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rsym value: 0.072
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7804 / Rsym value: 0.51 / % possible all: 93.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.94 Å
Translation2.5 Å49.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FJM

1fjm


Resolution: 1.63→26.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.143 / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.915 / SU B: 2.373 / SU ML: 0.046 / SU R Cruickshank DPI: 0.081 / SU Rfree: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 4185 5 %RANDOM
Rwork0.143 ---
obs0.144 79699 99.73 %-
all-83995 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.32 Å2 / Biso mean: 12.9 Å2 / Biso min: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.63→26.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 40 682 5475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225080
X-RAY DIFFRACTIONr_bond_other_d0.0010.023486
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9976926
X-RAY DIFFRACTIONr_angle_other_deg0.9338498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80923.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80515850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7321534
X-RAY DIFFRACTIONr_chiral_restr0.080.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021105
X-RAY DIFFRACTIONr_nbd_refined0.2190.21067
X-RAY DIFFRACTIONr_nbd_other0.2030.23896
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22526
X-RAY DIFFRACTIONr_nbtor_other0.0830.22603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2494
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.245
X-RAY DIFFRACTIONr_mcbond_it1.2333033
X-RAY DIFFRACTIONr_mcbond_other0.31831221
X-RAY DIFFRACTIONr_mcangle_it1.95454883
X-RAY DIFFRACTIONr_scbond_it3.06682229
X-RAY DIFFRACTIONr_scangle_it4.418112010
LS refinement shellResolution: 1.63→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 286 -
Rwork0.212 5611 -
all-5897 -
obs-5611 96.74 %
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)
11.1623-0.3391.11573.7081-0.46321.4901-0.0070.0562-0.0241-0.0529-0.00470.06670.0296-0.21190.0116-0.06980.0009-0.00510.0167-0.00780.0016-12.7446-25.5462-6.6025
20.2778-0.1707-0.37370.11590.30991.0877-0.02180.0929-0.0556-0.09690.0030.031-0.0198-0.02720.0188-0.05370.0035-0.0146-0.0032-0.0075-0.0089-3.7655-25.7022-7.5893
30.4826-0.0319-0.28370.652-0.01580.63320.0117-0.0494-0.01830.0816-0.0123-0.0082-0.01190.03460.0006-0.0552-0.0033-0.0065-0.01670.0102-0.0254-2.4146-24.06228.0421
40.3786-0.6727-0.05112.9493-0.4851.50310.0079-0.07020.21710.3724-0.0544-0.32-0.20340.21910.04650.0054-0.0451-0.04680.0368-0.01780.01317.9798-14.487816.5892
50.69650.0802-0.3130.90750.06380.5948-0.0581-0.1894-0.1170.2623-0.006-0.01420.06020.11470.06410.04440.0106-0.00790.0330.0426-0.0192-1.3289-32.803922.3471
63.00080.28651.7382.14520.14412.8855-0.0447-0.07090.07760.070.0138-0.0734-0.2190.11660.0309-0.027-0.009-0.0005-0.0427-0.0023-0.0081-29.0072-38.937246.0518
70.6595-0.0310.30890.7948-0.09491.3836-0.0099-0.07080.04490.0307-0.00240.0716-0.0334-0.06130.0122-0.0492-0.00150.001-0.04180.0141-0.006-36.3817-46.010141.9984
80.50580.1183-0.06830.6830.02870.6491-0.02470.02570.0124-0.09050.02090.0347-0.0078-0.01260.0038-0.0357-0.0056-0.005-0.05040.0151-0.021-32.01-47.793231.3207
90.4438-0.5127-0.57081.019-0.05231.9216-0.05640.1929-0.0774-0.2131-0.00940.22020.0234-0.37220.06570.0027-0.0297-0.06430.041-0.00240.0369-45.7654-52.083320.0553
100.79560.123-0.10010.7897-0.02260.5866-0.08110.1721-0.0427-0.25990.0468-0.06410.02210.02640.03430.0466-0.02310.01990.00410.0081-0.023-25.7101-50.615516.1721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 212 - 16
2X-RAY DIFFRACTION2AA22 - 4017 - 35
3X-RAY DIFFRACTION3AA41 - 18636 - 181
4X-RAY DIFFRACTION4AA187 - 200182 - 195
5X-RAY DIFFRACTION5AA201 - 299196 - 294
6X-RAY DIFFRACTION6BB7 - 212 - 16
7X-RAY DIFFRACTION7BB22 - 4917 - 44
8X-RAY DIFFRACTION8BB50 - 18145 - 176
9X-RAY DIFFRACTION9BB182 - 198177 - 193
10X-RAY DIFFRACTION10BB199 - 299194 - 294

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