[English] 日本語
Yorodumi
- PDB-7bbc: Joint X-ray/neutron room temperature structure of perdeuterated P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bbc
TitleJoint X-ray/neutron room temperature structure of perdeuterated PLL lectin in complex with perdeuterated L-fucose
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / Complex / propeller
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / alpha-L-fucopyranose / beta-L-fucopyranose / Uncharacterized protein
Function and homology information
Biological speciesPhotorhabdus laumondii (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
Funding support France, 1items
OrganizationGrant numberCountry
Institut Laue-Langevin France
CitationJournal: Structure / Year: 2021
Title: Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions.
Authors: Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9307
Polymers41,9451
Non-polymers9856
Water6,017334
1
A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,72028
Polymers167,7804
Non-polymers3,94024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)72.665, 89.210, 159.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

-
Components

#1: Protein PLL lectin


Mass: 41944.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: CKY10_20885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A329WTS5
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na/K tartrate dissolved in D2O, soaked with 50 mM perdeuterated fucose-d12 dissolved in D2O

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SEALED TUBEXenocs GeniX 3D Cu HF11.542
NUCLEAR REACTORILL LADI III23.07-4.05
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEJan 15, 2020
LADI III2IMAGE PLATEAug 4, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
23.071
34.051
Reflection

Biso Wilson estimate: 19.08 Å2 / Entry-ID: 7BBC

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.84-334527610011.510.11114.7
2.2-462234884.94.10.1628
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
1.84-1.880.5827660.831
2.2-2.320.3328222

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata processing
Aimlessdata scaling
SCALAdata scaling
PHENIXphasing
LAUEGENdata processing
LAUEGENdata reduction
LSCALEdata scaling
Refinement

Biso mean: 34.65 Å2 / % reflection Rfree: 5 % / SU ML: 0.1415 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 12.7897 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5c9o

5c9o

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)
1.84-33X-RAY DIFFRACTION0.13980.12130.12222265430064527199.9711.37
2.2-45.99NEUTRON DIFFRACTION0.22110.190611122223383.262
Refinement stepCycle: LAST / Resolution: 1.84→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 66 334 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01036680
X-RAY DIFFRACTIONf_angle_d1.322511152
X-RAY DIFFRACTIONf_chiral_restr0.0743499
X-RAY DIFFRACTIONf_plane_restr0.0072938
X-RAY DIFFRACTIONf_dihedral_angle_d13.96072382
NEUTRON DIFFRACTIONf_bond_d0.01036680
NEUTRON DIFFRACTIONf_angle_d1.322511152
NEUTRON DIFFRACTIONf_chiral_restr0.0743499
NEUTRON DIFFRACTIONf_plane_restr0.0072938
NEUTRON DIFFRACTIONf_dihedral_angle_d13.96072382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.24581400.2122658X-RAY DIFFRACTION99.75
1.88-1.920.2031400.16432659X-RAY DIFFRACTION100
1.92-1.970.17861390.13952653X-RAY DIFFRACTION100
1.97-2.020.1531400.12932640X-RAY DIFFRACTION100
2.02-2.080.14351400.13312673X-RAY DIFFRACTION100
2.08-2.150.16361390.13582647X-RAY DIFFRACTION100
2.15-2.230.15711410.1262673X-RAY DIFFRACTION100
2.23-2.320.14291410.11572661X-RAY DIFFRACTION100
2.32-2.420.15491400.11872682X-RAY DIFFRACTION100
2.42-2.550.13571410.11692674X-RAY DIFFRACTION100
2.55-2.710.17461420.13052692X-RAY DIFFRACTION100
2.71-2.920.16131410.13212681X-RAY DIFFRACTION100
2.92-3.210.13751420.12622698X-RAY DIFFRACTION100
3.21-3.680.11281430.11642712X-RAY DIFFRACTION100
3.68-4.630.09511440.09082750X-RAY DIFFRACTION100
4.63-330.12781520.10912853X-RAY DIFFRACTION99.77

+
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