[English] 日本語
Yorodumi
- PDB-5ida: Crystal structure of CGL1 from Crassostrea gigas, mannose-bound f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ida
TitleCrystal structure of CGL1 from Crassostrea gigas, mannose-bound form (CGL1/MAN)
ComponentsNatterin-3
KeywordsSUGAR BINDING PROTEIN / CGL1 / lectin / Crassostrea gigas / N-type / mannose
Function / homologyDM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / beta-D-mannopyranose / Natterin-3
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsUnno, H.
CitationJournal: Sci Rep / Year: 2016
Title: Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas.
Authors: Unno, H. / Matsuyama, K. / Tsuji, Y. / Goda, S. / Hiemori, K. / Tateno, H. / Hirabayashi, J. / Hatakeyama, T.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Derived calculations
Revision 1.3Feb 19, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Natterin-3
B: Natterin-3
C: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8557
Polymers62,3154
Non-polymers5403
Water12,809711
1
A: Natterin-3
C: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3383
Polymers31,1572
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Natterin-3
D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5184
Polymers31,1572
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Natterin-3
hetero molecules

D: Natterin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5184
Polymers31,1572
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_547-x,y-1/2,-z+21
MethodPISA
4
B: Natterin-3
hetero molecules

C: Natterin-3


Theoretical massNumber of molelcules
Total (without water)31,3383
Polymers31,1572
Non-polymers1801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)39.723, 58.778, 108.460
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#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
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, 20% PEG8000

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 160510 / % possible obs: 79.6 % / Redundancy: 3.9 % / Net I/σ(I): 17

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.1→17.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.505 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22207 8117 5.1 %RANDOM
Rwork0.1641 ---
obs0.16705 152237 79.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.04 Å2
2---0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.1→17.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 36 713 5109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0194501
X-RAY DIFFRACTIONr_bond_other_d0.0020.024256
X-RAY DIFFRACTIONr_angle_refined_deg2.4471.9576103
X-RAY DIFFRACTIONr_angle_other_deg2.3539795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.465560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.14924.468188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68915704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.051512
X-RAY DIFFRACTIONr_chiral_restr0.1950.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215108
X-RAY DIFFRACTIONr_gen_planes_other0.010.021028
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7472.2482265
X-RAY DIFFRACTIONr_mcbond_other1.7462.2472264
X-RAY DIFFRACTIONr_mcangle_it1.9033.3882816
X-RAY DIFFRACTIONr_mcangle_other1.9033.3882817
X-RAY DIFFRACTIONr_scbond_it3.1242.5272236
X-RAY DIFFRACTIONr_scbond_other3.1242.5272236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1763.6853287
X-RAY DIFFRACTIONr_long_range_B_refined3.42620.6055621
X-RAY DIFFRACTIONr_long_range_B_other2.98519.5055141
X-RAY DIFFRACTIONr_rigid_bond_restr6.69338757
X-RAY DIFFRACTIONr_sphericity_free24.3935128
X-RAY DIFFRACTIONr_sphericity_bonded9.36859237
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 771 -
Rwork0.214 13622 -
obs--97.24 %

+
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