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- PDB-6obq: PP1 H66K in complex with Microcystin LR -

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Basic information

Entry
Database: PDB / ID: 6obq
TitlePP1 H66K in complex with Microcystin LR
Components
  • Microcystin LR
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/TOXIN / phosphatase / HYDROLASE-TOXIN complex
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / histone H2AXS140 phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / dephosphorylation / glycogen metabolic process / myosin phosphatase activity / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / DARPP-32 events / transition metal ion binding / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / 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 ...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
Microcystin LR / : / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChoy, M.S. / Moon, T.M. / Bray, J.A. / Archuleta, T.L. / Shi, W. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: SDS22 selectively recognizes and traps metal-deficient inactive PP1.
Authors: Choy, M.S. / Moon, T.M. / Ravindran, R. / Bray, J.A. / Robinson, L.C. / Archuleta, T.L. / Shi, W. / Peti, W. / Tatchell, K. / Page, R.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn_type.id
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 / pdbx_validate_rmsd_bond / 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.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: Microcystin LR
D: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4456
Polymers70,3354
Non-polymers1102
Water5,224290
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2223
Polymers35,1672
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area11950 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2223
Polymers35,1672
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.916, 76.619, 130.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34153.184 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300 / Mutation: H66K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide Microcystin LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG6000, 1 M lithium chloride, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.84→22.04 Å / Num. obs: 57463 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.74
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 3512 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MOV

4mov


Resolution: 1.84→22.04 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.96
RfactorNum. reflection% reflection
Rfree0.2602 2888 5.04 %
Rwork0.2302 --
obs0.2317 57317 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→22.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 2 290 5059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034979
X-RAY DIFFRACTIONf_angle_d0.8646769
X-RAY DIFFRACTIONf_dihedral_angle_d10.5834004
X-RAY DIFFRACTIONf_chiral_restr0.045742
X-RAY DIFFRACTIONf_plane_restr0.007886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.87020.3671380.3312582X-RAY DIFFRACTION100
1.8702-1.90240.37841150.30712586X-RAY DIFFRACTION100
1.9024-1.9370.3161550.29452525X-RAY DIFFRACTION100
1.937-1.97420.34231560.29912559X-RAY DIFFRACTION100
1.9742-2.01450.33021420.28022563X-RAY DIFFRACTION100
2.0145-2.05820.30491250.27632562X-RAY DIFFRACTION100
2.0582-2.10610.33261100.27722574X-RAY DIFFRACTION100
2.1061-2.15870.32231290.27992574X-RAY DIFFRACTION100
2.1587-2.2170.29761340.27812582X-RAY DIFFRACTION100
2.217-2.28220.34791430.27352568X-RAY DIFFRACTION100
2.2822-2.35580.29351310.26752566X-RAY DIFFRACTION100
2.3558-2.43990.30311510.24942566X-RAY DIFFRACTION100
2.4399-2.53740.2991220.25742580X-RAY DIFFRACTION100
2.5374-2.65270.28591310.24372614X-RAY DIFFRACTION100
2.6527-2.79230.27781610.23712568X-RAY DIFFRACTION100
2.7923-2.96690.21751370.23852594X-RAY DIFFRACTION100
2.9669-3.19530.26291290.22392605X-RAY DIFFRACTION100
3.1953-3.51570.22851470.21362585X-RAY DIFFRACTION99
3.5157-4.02180.21861370.18612641X-RAY DIFFRACTION99
4.0218-5.05690.18291620.14742640X-RAY DIFFRACTION100
5.0569-22.04420.17511330.1712795X-RAY DIFFRACTION100

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