6GL5 | pdb_00006gl5

Crystal Structure of dimethylated RSL - sulfonatocalix[4]arene complex

PDB DOI: https://doi.org/10.2210/pdb6GL5/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-23 Released: 2019-06-19
Deposition Author(s): Guagnini, F., Rennie, M.L., Crowley, P.B.
Funding Organization(s): Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.182 (Depositor), 0.195 (DCC)
R-Value Work:
0.162 (Depositor), 0.176 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Protein Crystallization via Sulfonatocalix[4]arene Dimethylammonium Complexation

Guagnini, F., Antonik, P.M., Rennie, M.L., Pinalli, R., Dalcanale, E., Crowley, P.B.

To be published.

Macromolecule Content

Total Structure Weight: 35.33 kDa
Atom Count: 2,907
Modeled Residue Count: 270
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C	90	Ralstonia solanacearum	Mutation(s): 0 Gene Names: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T3Y (Subject of Investigation/LOI) Query on T3Y Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A] J [auth B] K [auth B] P [auth C] Q [auth C] D [auth A], J [auth B], K [auth B], P [auth C], Q [auth C], R [auth C]	25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid C₂₈ H₂₄ O₁₆ S₄ JFYBCAFLVNKHHG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B]	H [auth A], N [auth B], O [auth B], V [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] L [auth B] M [auth B] S [auth C] E [auth A], F [auth A], L [auth B], M [auth B], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B, C	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.182 (Depositor), 0.195 (DCC)
R-Value Work: 0.162 (Depositor), 0.176 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.92	α = 90
b = 67.57	β = 90
c = 87.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Guagnini, F.

Rennie, M.L.

Crowley, P.B.

Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/ERC/B2912 and 13/CDA/2168

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 2.0: 2020-08-05
Changes: Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description