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- PDB-2m83: Solution structure of the carbohydrate binding module of the musc... -

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Basic information

Entry
Database: PDB / ID: 2m83
TitleSolution structure of the carbohydrate binding module of the muscle glycogen-targeting subunit of Protein Phosphatase-1
ComponentsProtein phosphatase 1 regulatory subunit 3A
KeywordsHYDROLASE / protein / starch binding domain / carbohydrate binding module
Function / homology
Function and homology information


glycogen binding / protein phosphatase type 1 complex / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / glycogen metabolic process / membrane
Similarity search - Function
Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein phosphatase 1 regulatory subunit 3A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKoveal, D. / Page, R. / Peti, W.
CitationJournal: To be Published
Title: Molecular basis for Protein Phosphatase-1 regulation by the muscle glycogen-targeting subunit GM
Authors: Koveal, D. / Choy, M. / Page, R. / Peti, W.
History
DepositionMay 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1 regulatory subunit 3A


Theoretical massNumber of molelcules
Total (without water)15,9981
Polymers15,9981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein phosphatase 1 regulatory subunit 3A / Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen ...Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen targeting subunit / RG1


Mass: 15998.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PPP1R3A, PP1G / Production host: Escherichia coli (E. coli) / References: UniProt: Q00756

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCA
1523D (H)CC(CO)NH
1623D HBHA(CO)NH
1723D (H)CCH-TOCSY
1832D 1H-1H NOESY
1932D 1H-1H TOCSY
11032D 1H-1H COSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 15N] GM CBM21, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 13C; U-99% 15N] GM CBM21, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM GM CBM21, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMGM CBM21-1[U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
10 mMDTT-41
0.8 mMGM CBM21-5[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-62
50 mMsodium chloride-72
10 mMDTT-82
0.8 mMGM CBM21-93
20 mMsodium phosphate-103
50 mMsodium chloride-113
10 mMDTT-123
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANA_2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: RECOORD scripts were used (Nederveen et al. Proteins. 2005.)
NMR constraintsNOE constraints total: 2709 / NOE intraresidue total count: 177 / NOE long range total count: 767 / NOE medium range total count: 961 / NOE sequential total count: 804
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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