[English] 日本語
Yorodumi
- PDB-9ib9: Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ib9
TitleTumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with B Lewis b pentasaccharide
ComponentsPhotorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
KeywordsSUGAR BINDING PROTEIN / lectin / TNF-like / Photorhabdus laumondii / PLTL / fucose-binding
Function / homology: / Bc2l-C, N-terminal domain / : / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMelicher, F. / Wimmerova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
CitationJournal: Febs J. / Year: 2025
Title: Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.
Authors: Melicher, F. / Dobes, P. / Komarek, J. / Faltinek, L. / Korsak, M. / Sykorova, P. / Houser, J. / Wimmerova, M.
History
DepositionFeb 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
D: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
E: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
F: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,73712
Polymers89,7106
Non-polymers5,0276
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24650 Å2
ΔGint64 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.303, 166.979, 50.346
Angle α, β, γ (deg.)90.000, 106.629, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17


Mass: 14951.746 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu4240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MZP1
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-[alpha-L- ...alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 837.771 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Oligosaccharide with branches / References: BIRD: PRD_002591
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-3[LFucpa1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3-4-3/a3-b1_a4-e1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBlood group antigen composed of fucose, galactose and N-acetyl-beta-D-glucosamine. Branched amino ...Blood group antigen composed of fucose, galactose and N-acetyl-beta-D-glucosamine. Branched amino pentasaccharide consisting of linear trisaccharide, alpha-D-galactosyl-(1-3)-beta-D-galactosyl-(1-3)-N-acetyl-beta-D-glucosamine, with alpha-L-fucosyl residues attached at position 2 and position 4 of the trisaccharide.
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: trisodium citrate, PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→48.24 Å / Num. obs: 186694 / % possible obs: 96.2 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 12.6
Reflection shellResolution: 1.3→1.37 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 26429 / CC1/2: 0.693

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
SCALAdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→46.388 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.761 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1731 9353 5.012 %
Rwork0.1421 177249 -
all0.144 --
obs-186602 96.066 %
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: 16.149 Å2
Baniso -1Baniso -2Baniso -3
1-1.047 Å20 Å2-0.261 Å2
2---0.297 Å2-0 Å2
3----0.503 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6171 0 342 582 7095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166588
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.77410073
X-RAY DIFFRACTIONr_angle_other_deg0.5991.70615344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.689531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.816101060
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.34210282
X-RAY DIFFRACTIONr_chiral_restr0.0880.21273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028543
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021645
X-RAY DIFFRACTIONr_nbd_refined0.2550.21187
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.26191
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23583
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.23695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2386
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.220
X-RAY DIFFRACTIONr_nbd_other0.1680.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.21
X-RAY DIFFRACTIONr_mcbond_it4.8341.6163551
X-RAY DIFFRACTIONr_mcbond_other4.8251.6163551
X-RAY DIFFRACTIONr_mcangle_it6.7692.9144503
X-RAY DIFFRACTIONr_mcangle_other6.7722.9154504
X-RAY DIFFRACTIONr_scbond_it6.1474.2513704
X-RAY DIFFRACTIONr_scbond_other6.1464.253705
X-RAY DIFFRACTIONr_scangle_it8.56213.0135524
X-RAY DIFFRACTIONr_scangle_other8.56113.0115525
X-RAY DIFFRACTIONr_lrange_it11.506669.5067787
X-RAY DIFFRACTIONr_lrange_other11.505669.4227788
X-RAY DIFFRACTIONr_rigid_bond_restr3.566313836
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
1.3-1.3340.2686680.231127490.233143200.9590.97293.69410.222
1.334-1.370.2386650.202123060.204139670.9660.97892.86890.189
1.37-1.410.2226370.17122560.172135780.9730.98494.95510.156
1.41-1.4530.1986350.145119500.148132080.9780.98895.28320.132
1.453-1.5010.1845920.136116750.139128280.980.9995.62680.123
1.501-1.5540.1795710.12112330.122123310.9810.99295.72620.107
1.554-1.6120.1625250.108110230.111120040.9830.99396.20130.098
1.612-1.6780.155590.101105870.103115570.9870.99496.44370.092
1.678-1.7520.165270.102100140.105109490.9840.99496.27360.095
1.752-1.8380.1594830.11394510.115105610.9830.99394.06310.106
1.838-1.9370.175210.1293270.123101160.9820.99297.35070.116
1.937-2.0540.1654640.13487330.13594020.9840.99197.81960.131
2.054-2.1960.1764830.14383070.14589760.9830.98997.92780.143
2.196-2.3710.173620.13477460.13682750.9830.9997.98190.135
2.371-2.5970.1734180.13771190.13976700.9820.98998.2660.14
2.597-2.9020.1693600.14764690.14869180.9830.98798.71350.152
2.902-3.3490.1662740.15455530.15561570.9840.98694.64030.163
3.349-4.0970.1662730.14848360.14951410.9830.98899.37760.161
4.097-5.7710.1542180.14437910.14440240.9910.99299.62720.16
5.771-46.3880.2141180.20521240.20622580.9810.98399.29140.219

+
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