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- PDB-4kq1: Crystal structure of yeast glycogen synthase in complex with urid... -

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Basic information

Entry
Database: PDB / ID: 4kq1
TitleCrystal structure of yeast glycogen synthase in complex with uridine-5'-monophosphate
ComponentsGsy2p
KeywordsTRANSFERASE / Glycosyltransferase / GT-B / Rossmann Fold / glucosylation
Function / homology
Function and homology information


F1FO ATP Synthase / F1FO ATP Synthase - #10 / Glycogen Phosphorylase B; / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / URIDINE-5'-MONOPHOSPHATE / :
Similarity search - Component
Biological speciesSaccharomyces cerevisiae FostersO (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsChikwana, V.M. / Hurley, T.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase.
Authors: Chikwana, V.M. / Khanna, M. / Baskaran, S. / Tagliabracci, V.S. / Contreras, C.J. / Depaoli-Roach, A. / Roach, P.J. / Hurley, T.D.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gsy2p
B: Gsy2p
C: Gsy2p
D: Gsy2p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,00516
Polymers328,2434
Non-polymers2,76212
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17350 Å2
ΔGint-87 kcal/mol
Surface area98090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.089, 204.372, 206.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLYAA2 - 20521 - 224
211SERSERGLYGLYBB2 - 20521 - 224
311SERSERGLYGLYCC2 - 20521 - 224
411SERSERGLYGLYDD2 - 20521 - 224
121ASPASPALAALAAA208 - 278227 - 297
221ASPASPALAALABB208 - 278227 - 297
321ASPASPALAALACC208 - 278227 - 297
421ASPASPALAALADD208 - 278227 - 297
131TRPTRPALAALAAA599 - 639618 - 658
231TRPTRPALAALABB599 - 639618 - 658
331TRPTRPALAALACC599 - 639618 - 658
431TRPTRPALAALADD599 - 639618 - 658
112PHEPHEASPASPAA279 - 598298 - 617
212PHEPHEASPASPBB279 - 598298 - 617
312PHEPHEASPASPCC279 - 598298 - 617
412PHEPHEASPASPDD279 - 598298 - 617

NCS ensembles :
ID
1
2

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Components

#1: Protein
Gsy2p


Mass: 82060.719 Da / Num. of mol.: 4 / Mutation: R589A, R592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae FostersO (yeast)
Strain: strain ATCC 204508 / S288c / Gene: FOSTERSO_3265, GSY2 YLR258W L8479.8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E7NKU1, glycogen(starch) synthase
#2: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3

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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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 0.1 M Bis-Tris, 16% PEG 300, pH 6.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. all: 117070 / Num. obs: 111217 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 5.7 % / Biso Wilson estimate: 69.509583 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.022 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.66-2.714.40.6651250.882188.4
2.71-2.7650.5954150.914193.7
2.76-2.815.30.51855010.942194.4
2.81-2.875.80.46656160.971196.4
2.87-2.935.80.3956230.977196.9
2.93-35.80.35256351.007197.1
3-3.075.90.2956411.054196.9
3.07-3.155.90.23856091.067196.7
3.15-3.255.90.18156551.065196.6
3.25-3.355.90.14756171.097196.4
3.35-3.475.90.11855941.087196.2
3.47-3.615.90.09956001.042196
3.61-3.775.90.08456101.089195.9
3.77-3.975.90.07356101.099195.5
3.97-4.225.90.06455721.003195.3
4.22-4.555.90.05955720.991194.9
4.55-55.80.05755740.99194.5
5-5.735.80.06255451.082194
5.73-7.215.70.05455670.979193.3
7.21-505.60.03655361.011190.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NB0

3nb0


Resolution: 2.66→48.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.395 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.548 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 5574 5 %RANDOM
Rwork0.2085 ---
obs0.2111 111215 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.04 Å2 / Biso mean: 80.9411 Å2 / Biso min: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1--4.23 Å2-0 Å20 Å2
2--9.42 Å20 Å2
3----5.19 Å2
Refinement stepCycle: LAST / Resolution: 2.66→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20563 0 176 0 20739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01921237
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.95428785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62752545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15323.5991067
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59153558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.25315156
X-RAY DIFFRACTIONr_chiral_restr0.0880.23134
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116257
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2536MEDIUM POSITIONAL0.510.5
12B2536MEDIUM POSITIONAL0.50.5
13C2536MEDIUM POSITIONAL0.490.5
14D2536MEDIUM POSITIONAL0.510.5
11A2536MEDIUM THERMAL14.672
12B2536MEDIUM THERMAL17.92
13C2536MEDIUM THERMAL16.382
14D2536MEDIUM THERMAL24.482
21A2592MEDIUM POSITIONAL0.360.5
22B2592MEDIUM POSITIONAL0.380.5
23C2592MEDIUM POSITIONAL0.410.5
24D2592MEDIUM POSITIONAL0.360.5
21A2592MEDIUM THERMAL10.692
22B2592MEDIUM THERMAL12.312
23C2592MEDIUM THERMAL9.642
24D2592MEDIUM THERMAL8.612
LS refinement shellResolution: 2.657→2.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 421 -
Rwork0.348 7354 -
all-7775 -
obs--90.13 %

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