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- PDB-7qfa: Monoclinic crystal structure of PTG CBM21 in complex with beta-cy... -

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Basic information

Entry
Database: PDB / ID: 7qfa
TitleMonoclinic crystal structure of PTG CBM21 in complex with beta-cyclodextrin
ComponentsProtein phosphatase 1 regulatory subunit 3C
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding / immunoglobulin-like fold
Function / homology
Function and homology information


glycogen binding / regulation of glycogen biosynthetic process / protein phosphatase type 1 complex / protein phosphatase 1 binding / glycogen biosynthetic process / protein serine/threonine phosphatase activity / glycogen metabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding ...glycogen binding / regulation of glycogen biosynthetic process / protein phosphatase type 1 complex / protein phosphatase 1 binding / glycogen biosynthetic process / protein serine/threonine phosphatase activity / glycogen metabolic process / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding / molecular adaptor activity / cytosol
Similarity search - Function
Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / 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
beta-cyclodextrin / Protein phosphatase 1 regulatory subunit 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSemrau, M.S. / Storici, P. / Lolli, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular architecture of the glycogen- committed PP1/PTG holoenzyme.
Authors: Semrau, M.S. / Giachin, G. / Covaceuszach, S. / Cassetta, A. / Demitri, N. / Storici, P. / Lolli, G.
History
DepositionDec 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase 1 regulatory subunit 3C
B: Protein phosphatase 1 regulatory subunit 3C
C: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,77010
Polymers46,9433
Non-polymers3,8277
Water4,252236
1
A: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8012
Polymers15,6481
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0775
Polymers15,6481
Non-polymers1,4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8933
Polymers15,6481
Non-polymers1,2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.830, 42.866, 168.994
Angle α, β, γ (deg.)90.000, 100.670, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))
21(chain B and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))
31(chain C and (resid 3 through 81 or resid 83 through 129))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))A3 - 76
121(chain A and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))A80 - 81
131(chain A and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))A83 - 129
211(chain B and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))B3 - 76
221(chain B and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))B80 - 81
231(chain B and (resid 3 through 76 or resid 80 through 81 or resid 83 through 129))B83 - 129
311(chain C and (resid 3 through 81 or resid 83 through 129))C3 - 81
321(chain C and (resid 3 through 81 or resid 83 through 129))C83 - 129

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Components

#1: Protein Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 5 / PP1 subunit R5 / Protein targeting to glycogen / PTG


Mass: 15647.529 Da / Num. of mol.: 3 / Fragment: CBM21 domain (residues 132-264) / Mutation: First residue S derives from the expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3C, PPP1R5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQK1
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.45 % / Mosaicity: 0.17 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2→46.81 Å / Num. obs: 31810 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 12 / Num. measured all: 208427 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.60.9531546023380.7780.3991.0352.298.7
8.94-46.815.40.03820423800.9970.0180.04336.196.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEF

2eef


Resolution: 2→41.506 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 1554 4.89 %
Rwork0.1731 30248 -
obs0.175 31802 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 37.8908 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 2→41.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 255 236 3604
Biso mean--31.83 43.03 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073470
X-RAY DIFFRACTIONf_angle_d1.0574741
X-RAY DIFFRACTIONf_chiral_restr0.069577
X-RAY DIFFRACTIONf_plane_restr0.005563
X-RAY DIFFRACTIONf_dihedral_angle_d15.6121889
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1744X-RAY DIFFRACTION18.257TORSIONAL
12B1744X-RAY DIFFRACTION18.257TORSIONAL
13C1744X-RAY DIFFRACTION18.257TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06460.25281450.2181268998
2.0646-2.13840.28591390.2206274898
2.1384-2.2240.27181350.2049271099
2.224-2.32520.25971360.197273799
2.3252-2.44770.23591470.1904271699
2.4477-2.60110.23071450.1824274899
2.6011-2.80190.21811380.1777275799
2.8019-3.08380.23991520.1841274999
3.0838-3.52980.21371380.1637277999
3.5298-4.44630.17431490.1491275598
4.4463-41.5060.17831300.1625286098
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)
12.2869-0.94921.21733.1680.22063.28650.08790.2618-0.3729-0.2482-0.07410.00950.29620.1082-0.02540.27790.0327-0.00440.2142-0.0120.245918.5194-7.267927.8979
23.4925-1.74311.2891.372-0.90063.00120.0054-0.293-0.05350.04630.11920.1732-0.239-0.2903-0.09090.18550.00750.02080.1733-0.00450.218714.08850.873237.9894
37.3772-0.0716-0.33261.08621.01390.98190.25340.5253-0.05230.45770.00540.31660.61220.1451-0.17480.36560.0639-0.04330.4081-0.0640.345228.9568-14.708340.0246
42.9021-1.12870.37322.40510.14311.8794-0.00310.1269-0.169-0.1879-0.02780.1509-0.1804-0.13170.04430.21280.0221-0.00580.17880.00640.239611.9459-0.702229.7503
52.4393-0.91320.17682.01241.14553.69260.0536-0.18040.18490.0574-0.03970.2031-0.5052-0.17280.0210.240.0583-0.00190.2938-0.01180.290940.4139-15.844626.2218
62.4310.69740.86211.8061-1.4784.12380.01920.0687-0.0037-0.22960.0764-0.00410.2136-0.301-0.11020.17960.01720.02650.2664-0.04440.216144.7885-25.389719.6229
71.19960.8941-0.19561.4788-0.36141.73180.1356-0.34690.008-0.0281-0.22460.03750.24080.05510.09890.1903-0.00860.0110.3301-0.00030.26941.5156-27.078727.5587
82.9041-0.191-0.46792.07970.10373.16620.0747-0.2980.36260.0419-0.00430.0406-0.0864-0.02530.01090.22730.02860.00140.3537-0.03330.275846.972-20.784129.8499
92.5107-0.3990.7140.85620.37533.0761-0.01490.0240.1434-0.01420.08850.0191-0.4647-0.1974-0.06430.38830.03340.00790.2366-0.01750.26464.7072-16.66549.0067
100.88290.209-0.52353.4541-0.83824.57-0.0376-0.0190.0232-0.01470.1383-0.0376-0.3050.5883-0.16830.3269-0.0256-0.01530.3159-0.02870.252616.2377-19.056313.7475
112.67410.1536-0.15251.17280.16592.9590.08090.19870.1007-0.0079-0.05330.0062-0.64410.49220.00740.4201-0.0488-0.00460.2714-0.00190.218913.9917-14.8586.6574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 176 )A133 - 176
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 204 )A177 - 204
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 212 )A205 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 261 )A213 - 261
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 176 )B133 - 176
6X-RAY DIFFRACTION6chain 'B' and (resid 177 through 212 )B177 - 212
7X-RAY DIFFRACTION7chain 'B' and (resid 213 through 240 )B213 - 240
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 260 )B241 - 260
9X-RAY DIFFRACTION9chain 'C' and (resid 133 through 176 )C133 - 176
10X-RAY DIFFRACTION10chain 'C' and (resid 177 through 212 )C177 - 212
11X-RAY DIFFRACTION11chain 'C' and (resid 213 through 259 )C213 - 259

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