[English] 日本語
Yorodumi
- PDB-2qzs: Crystal Structure of Wild-type E.coli GS in complex with ADP and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qzs
TitleCrystal Structure of Wild-type E.coli GS in complex with ADP and Glucose(wtGSb)
Componentsglycogen synthase
KeywordsTRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and glucose binding / Glycogen biosynthesis / Glycosyltransferase
Function / homology
Function and homology information


starch synthase (glycosyl-transferring) / alpha-1,4-glucan glucosyltransferase (ADP-glucose donor) activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen biosynthetic process / DNA damage response / cytosol
Similarity search - Function
Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-250 / ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / Glycogen synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSheng, F. / Geiger, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Crystal Structures of the Open and Catalytically Competent Closed Conformation of Escherichia coli Glycogen Synthase.
Authors: Sheng, F. / Jia, X. / Yep, A. / Preiss, J. / Geiger, J.H.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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.name / _chem_comp.type ..._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 1.4Aug 30, 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 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8274
Polymers53,9511
Non-polymers8763
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.494, 126.494, 151.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

-
Components

#1: Protein glycogen synthase / Starch [bacterial glycogen] synthase


Mass: 53951.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6U8, starch synthase (glycosyl-transferring)
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-250 / (2R)-2-hydroxy-3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid


Mass: 268.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 40%(w/v) PEG 4000, 0.2 M Na tartrate, 0.1 M HEPPSO, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60327 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.057 / Χ2: 1.184 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.4 / Num. unique all: 6012 / Χ2: 0.794 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.299 / Cor.coef. Fo:Fc: 0.735
Highest resolutionLowest resolution
Rotation3 Å44.72 Å
Translation3 Å44.72 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZU

1rzu


Resolution: 2.2→44.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.519 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 5.36 / ESU R: 0.141 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3049 5.1 %RANDOM
Rwork0.203 ---
obs0.204 60312 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 56 208 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223892
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9685298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51822.849179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89415594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9571530
X-RAY DIFFRACTIONr_chiral_restr0.1360.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022996
X-RAY DIFFRACTIONr_nbd_refined0.2380.31871
X-RAY DIFFRACTIONr_nbtor_refined0.3250.52644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5411
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.520
X-RAY DIFFRACTIONr_mcbond_it1.16622427
X-RAY DIFFRACTIONr_mcangle_it1.82933769
X-RAY DIFFRACTIONr_scbond_it1.19721694
X-RAY DIFFRACTIONr_scangle_it1.63231529
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 233 -
Rwork0.214 4243 -
all-4476 -
obs-6012 99.31 %

+
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