4CE8

Perdeuterated Pseudomonas aeruginosa Lectin II complex with hydrogenated L-Fucose and Calcium

PDB DOI: https://doi.org/10.2210/pdb4CE8/pdb

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

Deposited: 2013-11-10 Released: 2014-11-12
Deposition Author(s): Cuypers, M.G., Mitchell, E.P., Mossou, E., Pokorna, M., Wimmerova, M., Imberty, A., Moulin, M., Haertlein, M., Forsyth, V.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free: 0.141
R-Value Work: 0.125
R-Value Observed: 0.126

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Perdeuterated Pseudomonas Aeruginosa Lectin II Complex with Hydrogenated L Fucose and Calcium

Cuypers, M.G., Mossou, E., Mitchell, E.P., Russi, S., Pokorna, M., Wimmerova, M., Imberty, A., Mcsweeney, S., Haertlein, M., Forsyth, V.T.

To be published.

Macromolecule Content

Total Structure Weight: 48.84 kDa
Atom Count: 4,775
Modelled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	114	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5 Go to UniProtKB: Q9HYN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain V [auth D] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C]	G [auth A], L [auth B], Q [auth C], V [auth D]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	H [auth A] I [auth A] M [auth B] N [auth B] R [auth C] H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
URE Query on URE Download Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain F [auth A] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C]	E [auth A] F [auth A] J [auth B] K [auth B] O [auth C] E [auth A], F [auth A], J [auth B], K [auth B], O [auth C], P [auth C], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free: 0.141
R-Value Work: 0.125
R-Value Observed: 0.126
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.48	α = 90
b = 72.49	β = 94.1
c = 54.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2016-09-28
Changes: Database references
Version 1.2: 2019-05-08
Changes: Advisory, Data collection, Experimental preparation, Other
Version 2.0: 2019-10-23
Changes: Atomic model, Data collection, Other
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2023-12-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary