[English] 日本語
Yorodumi
- PDB-3nb0: Glucose-6-Phosphate activated form of Yeast Glycogen Synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nb0
TitleGlucose-6-Phosphate activated form of Yeast Glycogen Synthase
ComponentsGlycogen [starch] synthase isoform 2
KeywordsTRANSFERASE / Glycogen Synthase / Glucose-6-phosphate / Yeast / Allosteric activation
Function / homology
Function and homology information


Glycogen synthesis / glycogen(starch) synthase / glycogen (starch) synthase activity / glycogen biosynthetic process / molecular function inhibitor activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
F1FO ATP Synthase / F1FO ATP Synthase - #10 / Glycogen synthase / Glycogen synthase / 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 / Glycogen [starch] synthase isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsBaskaran, S. / Hurley, T.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for glucose-6-phosphate activation of glycogen synthase.
Authors: Baskaran, S. / Roach, P.J. / Depaoli-Roach, A.A. / Hurley, T.D.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 6, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen [starch] synthase isoform 2
B: Glycogen [starch] synthase isoform 2
C: Glycogen [starch] synthase isoform 2
D: Glycogen [starch] synthase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,99316
Polymers328,7954
Non-polymers2,19812
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16430 Å2
ΔGint-71 kcal/mol
Surface area99550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.739, 206.982, 205.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
Glycogen [starch] synthase isoform 2


Mass: 82198.867 Da / Num. of mol.: 4 / Mutation: R589A R592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSY2, L8479.8, YLR258W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P27472, glycogen(starch) synthase
#2: 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ...THE CRYSTALLIZED SEQUENCE HAS BEEN REFERENCED TO UNP ENTRY P27472. HOWEVER, RESIDUE A535S IS ANNOTATED IN REMARK 999 GENBANK ENTRY ACCESSION CODE AAA88716

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Bis-Tris pH 6.2, 25% PEG 300, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 159580 / Num. obs: 157186 / % possible obs: 98.5 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 4.8 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.062 / Net I/σ(I): 15.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.552 / Num. unique all: 6244 / Χ2: 1.092 / % possible all: 79.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NAZ

3naz


Resolution: 2.406→46.229 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.816 / SU ML: 2.37 / Isotropic thermal model: Isotropic / Cross valid method: Thoughout / σ(F): 0.06 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 7445 5.02 %Random
Rwork0.211 ---
obs0.213 148274 93.56 %-
all-158090 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.359 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 115.97 Å2 / Biso mean: 57.191 Å2 / Biso min: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1--4.834 Å2-0 Å20 Å2
2---9.855 Å2-0 Å2
3---14.689 Å2
Refinement stepCycle: LAST / Resolution: 2.406→46.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20667 0 138 524 21329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421375
X-RAY DIFFRACTIONf_angle_d0.73728968
X-RAY DIFFRACTIONf_chiral_restr0.0543123
X-RAY DIFFRACTIONf_plane_restr0.0033747
X-RAY DIFFRACTIONf_dihedral_angle_d17.7497893
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.406-2.4330.3332000.283689388974
2.433-2.4620.2862060.2644166437284
2.462-2.4920.3112200.2554249446985
2.492-2.5230.3012370.2584252448986
2.523-2.5570.2962440.2634290453487
2.557-2.5920.3082470.264419466689
2.592-2.6290.292550.2514400465589
2.629-2.6680.2752390.2474487472690
2.668-2.710.3242360.244499473591
2.71-2.7540.2872520.2454570482292
2.754-2.8020.32140.2394616483092
2.802-2.8520.2712670.2414658492594
2.852-2.9070.2852460.244685493194
2.907-2.9670.2612630.2424710497394
2.967-3.0310.2882520.2394755500796
3.031-3.1020.2592410.2444826506797
3.102-3.1790.292500.2494915516597
3.179-3.2650.2732460.2334843508998
3.265-3.3610.2762580.2374965522398
3.361-3.470.2442480.2174920516899
3.47-3.5940.2332750.214944521999
3.594-3.7370.2212700.1924997526799
3.737-3.9080.222740.1944959523399
3.908-4.1130.212570.1844983524099
4.113-4.3710.2172480.1815066531499
4.371-4.7080.1992780.1735003528199
4.708-5.1810.2072170.1725057527499
5.181-5.930.222720.1935040531299
5.93-7.4660.2092600.1915080534099
7.466-46.2380.1942730.1744786505991

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more