[English] 日本語
Yorodumi
- PDB-1ll0: Crystal Structure of Rabbit Muscle Glycogenin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ll0
TitleCrystal Structure of Rabbit Muscle Glycogenin
ComponentsGLYCOGENIN-1
KeywordsTRANSFERASE / beta-alpha-beta Rossman-like nucleotide binding fold / DxD motif
Function / homology
Function and homology information


glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.43 Å
AuthorsGibbons, B.J. / Roach, P.J. / Hurley, T.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin.
Authors: Gibbons, B.J. / Roach, P.J. / Hurley, T.D.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGENIN-1
B: GLYCOGENIN-1
C: GLYCOGENIN-1
D: GLYCOGENIN-1
E: GLYCOGENIN-1
F: GLYCOGENIN-1
G: GLYCOGENIN-1
H: GLYCOGENIN-1
I: GLYCOGENIN-1
J: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)380,68610
Polymers380,68610
Non-polymers00
Water00
1
A: GLYCOGENIN-1
B: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)76,1372
Polymers76,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-23 kcal/mol
Surface area22570 Å2
MethodPISA
2
C: GLYCOGENIN-1
D: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)76,1372
Polymers76,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-23 kcal/mol
Surface area22060 Å2
MethodPISA
3
E: GLYCOGENIN-1
F: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)76,1372
Polymers76,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-23 kcal/mol
Surface area21830 Å2
MethodPISA
4
G: GLYCOGENIN-1
H: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)76,1372
Polymers76,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-23 kcal/mol
Surface area22320 Å2
MethodPISA
5
I: GLYCOGENIN-1
J: GLYCOGENIN-1


Theoretical massNumber of molelcules
Total (without water)76,1372
Polymers76,1372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-23 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.460, 139.460, 416.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
GLYCOGENIN-1


Mass: 38068.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P13280, glycogenin glucosyltransferase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 8-10 mg/mL glycogenin, 0.7 to 1.2 M ammonium sulphate, and 100 mM sodium phosphate buffer pH 6.6 to 6.9, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 6.9 / PH range high: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-10 mg/mlglycogenin1reservoir
20.7-1.2 Mammonium sulfate1reservoir
3100 mMsodium phosphate1reservoirpH6.6-6.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9794, 0.9322
DetectorType: SBC-2 / Detector: CCD / Date: Jun 1, 2000 / Details: Rosenbaum-Rock monochromators and focusing mirror
RadiationMonochromator: Monochromator 1: sagittal focusing Si(220)/Monochromator 2: sagittal focusing Si (111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
30.93221
ReflectionResolution: 3.43→50 Å / Num. obs: 56152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.088 / Net I/σ(I): 26
Reflection shellResolution: 3.43→3.52 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4.2 / Num. unique all: 56152 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 403861 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.484

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.43→25 Å / σ(F): 0.5 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2707 4.8 %RANDOM
Rwork0.252 ---
all0.254 ---
obs0.254 53593 95.8 %-
Displacement parametersBiso mean: 79.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.43→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20736 0 0 0 20736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_dihedral_angle_d23.38
X-RAY DIFFRACTIONc_improper_angle_d1.71
Refinement
*PLUS
Highest resolution: 3.43 Å / Lowest resolution: 25 Å / Rfactor all: 0.254 / Rfactor obs: 0.252 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.38
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.71

+
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://pdbjlvh1.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