[English] 日本語
Yorodumi
- PDB-8je9: Crystal structure of CGL1 from Crassostrea gigas, mannobiose-boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8je9
TitleCrystal structure of CGL1 from Crassostrea gigas, mannobiose-bound form (CGL1/Man(alpha)1-2Man)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / complex structure
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / ACETIC ACID / CACODYLATE ION / alpha-D-mannopyranose / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsUnno, H. / Hatakeyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: J.Biochem. / Year: 2023
Title: Mannose oligosaccharide recognition of CGL1, a mannose-specific lectin containing DM9 motifs from Crassostrea gigas, revealed by X-ray crystallographic analysis.
Authors: Hatakeyama, T. / Masuda, K. / Kudo, M. / Tanaka, K. / Takeuchi, A. / Unno, H.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Natterin-3
B: Natterin-3
C: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49711
Polymers62,3154
Non-polymers1,1827
Water14,448802
1
A: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8776
Polymers31,1572
Non-polymers7194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-1 kcal/mol
Surface area11570 Å2
MethodPISA
2
B: Natterin-3
C: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6205
Polymers31,1572
Non-polymers4623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-2 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.749, 58.701, 108.405
Angle α, β, γ (deg.)90.000, 93.701, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Natterin-3


Mass: 15578.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Crassostrea gigas (Pacific oyster) / References: UniProt: K1QRB6

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 806 molecules

#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 802 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate (pH 6.5), 20% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→39.8 Å / Num. obs: 229413 / % possible obs: 85.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.6
Reflection shellResolution: 1→1.02 Å / Num. unique obs: 4020 / CC1/2: 0.872

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→39.778 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.192 / Average fsc free: 0.9723 / Average fsc work: 0.976 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1869 11557 5.038 %
Rwork0.1744 217829 -
all0.175 --
obs-229386 85.767 %
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: 10.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20.013 Å2
2--0.007 Å2-0 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1→39.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 75 802 5237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124602
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164183
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6516255
X-RAY DIFFRACTIONr_angle_other_deg1.0171.5679758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.519516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51710721
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.98410192
X-RAY DIFFRACTIONr_chiral_restr0.1070.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025181
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02903
X-RAY DIFFRACTIONr_nbd_refined0.2050.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.23764
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22280
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1060.22362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2416
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3630.239
X-RAY DIFFRACTIONr_nbd_other0.2840.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.2168
X-RAY DIFFRACTIONr_mcbond_it1.0951.0532293
X-RAY DIFFRACTIONr_mcbond_other1.0951.0532293
X-RAY DIFFRACTIONr_mcangle_it1.4661.592849
X-RAY DIFFRACTIONr_mcangle_other1.4661.592850
X-RAY DIFFRACTIONr_scbond_it1.2311.2692309
X-RAY DIFFRACTIONr_scbond_other1.2331.2692310
X-RAY DIFFRACTIONr_scangle_it1.6151.8233395
X-RAY DIFFRACTIONr_scangle_other1.6151.8233396
X-RAY DIFFRACTIONr_lrange_it2.76735.8575299
X-RAY DIFFRACTIONr_lrange_other2.76735.8565299
X-RAY DIFFRACTIONr_rigid_bond_restr14.95638785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1-1.0260.2773680.27963100.279197660.9430.94633.78530.25
1.026-1.0540.2754900.25695520.257191370.9450.95752.47430.228
1.054-1.0850.2356880.235137740.235186820.9640.96577.41140.211
1.085-1.1180.2267410.215156360.216181240.9660.9790.36080.194
1.118-1.1550.2088230.204152630.204176070.9730.97391.36140.188
1.155-1.1960.2187800.199148890.2170220.970.97592.05150.186
1.196-1.2410.2177560.197144960.198164800.970.97592.54850.184
1.241-1.2910.2117480.198139540.199157700.9730.97593.22760.188
1.291-1.3490.2146810.194135300.195151430.9710.97693.84530.187
1.349-1.4140.2057020.184130590.185145670.9730.97894.46690.181
1.414-1.4910.27060.174123450.175137530.9750.98194.89570.174
1.491-1.5810.1816110.167119440.168131220.9810.98395.6790.174
1.581-1.690.1766360.163111480.164122620.9810.98496.10180.175
1.69-1.8250.1765890.157105070.158114690.9810.98596.74780.177
1.825-1.9990.1745570.16296960.163105510.9820.98497.17560.189
1.999-2.2340.1964810.16188530.16395520.9780.98497.71780.197
2.234-2.5780.1744030.16578960.16584460.9820.98498.25950.208
2.578-3.1550.1773460.16767280.16871620.9820.98398.77130.22
3.155-4.4470.1523020.1552530.15156060.9870.98799.09030.205
4.447-39.7780.1731490.17729960.17731640.9760.98499.39950.254

+
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