[English] 日本語
Yorodumi
- PDB-8xn6: The Crystal Structure of GSK3b from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xn6
TitleThe Crystal Structure of GSK3b from Biortus.
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / Photosynthesis
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesTrieres chinensis (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Wu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of GSK3b from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Wu, B.
History
DepositionDec 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,06527
Polymers93,5682
Non-polymers2,49725
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-20 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.694, 85.429, 178.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glycogen synthase kinase-3 beta


Mass: 46784.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trieres chinensis (Diatom) / Gene: GSK3B / Production host: Escherichia coli (E. coli)
References: tau-protein kinase, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 304 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 5% Glycerol, 20mM MgCl2, 100mM Hepes pH 7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2.4→48.75 Å / Num. obs: 50034 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.8
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 1.039 / Num. unique obs: 3441

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.751 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.818 / SU ML: 0.172 / Cross valid method: FREE R-VALUE / ESU R: 0.241 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2424 2516 5.029 %
Rwork0.1917 47518 -
all0.194 --
obs-50034 99.763 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.962 Å2
Baniso -1Baniso -2Baniso -3
1-1.789 Å20 Å20 Å2
2--3.097 Å20 Å2
3----4.885 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 157 279 6112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135965
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175739
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.6678069
X-RAY DIFFRACTIONr_angle_other_deg1.0871.57613222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18621.046306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10115990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4531547
X-RAY DIFFRACTIONr_chiral_restr0.0510.2770
X-RAY DIFFRACTIONr_chiral_restr_other0.0330.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021358
X-RAY DIFFRACTIONr_nbd_refined0.1890.21094
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.25070
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22853
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0660.213
X-RAY DIFFRACTIONr_nbd_other0.1290.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.24
X-RAY DIFFRACTIONr_mcbond_it2.9316.1062835
X-RAY DIFFRACTIONr_mcbond_other2.936.1052834
X-RAY DIFFRACTIONr_mcangle_it4.9229.1473539
X-RAY DIFFRACTIONr_mcangle_other4.9229.1493540
X-RAY DIFFRACTIONr_scbond_it3.0036.6063130
X-RAY DIFFRACTIONr_scbond_other3.0026.6063131
X-RAY DIFFRACTIONr_scangle_it4.9459.6754529
X-RAY DIFFRACTIONr_scangle_other4.9449.6754530
X-RAY DIFFRACTIONr_lrange_it10.123111.54323330
X-RAY DIFFRACTIONr_lrange_other10.124111.61423202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3462020.2933441X-RAY DIFFRACTION99.8356
2.462-2.530.2991940.283389X-RAY DIFFRACTION99.9442
2.53-2.6030.3221790.2533287X-RAY DIFFRACTION100
2.603-2.6830.2781650.2393200X-RAY DIFFRACTION100
2.683-2.7710.251460.223122X-RAY DIFFRACTION99.7254
2.771-2.8680.2461350.2172998X-RAY DIFFRACTION99.3657
2.868-2.9760.2641750.212883X-RAY DIFFRACTION99.674
2.976-3.0980.2751630.1962763X-RAY DIFFRACTION99.8976
3.098-3.2350.2531300.1932702X-RAY DIFFRACTION99.8942
3.235-3.3930.2171380.1862592X-RAY DIFFRACTION99.9268
3.393-3.5760.1931170.182479X-RAY DIFFRACTION99.8462
3.576-3.7930.2061210.1732312X-RAY DIFFRACTION99.9589
3.793-4.0540.2321270.1682183X-RAY DIFFRACTION99.6119
4.054-4.3780.1981190.1582026X-RAY DIFFRACTION99.5822
4.378-4.7950.217830.1551914X-RAY DIFFRACTION100
4.795-5.3590.244990.1711727X-RAY DIFFRACTION100
5.359-6.1840.268750.1911532X-RAY DIFFRACTION99.8757
6.184-7.5650.27750.1981310X-RAY DIFFRACTION99.4257
7.565-100.169430.1551049X-RAY DIFFRACTION99.0027

+
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