5OD5 | pdb_00005od5

Periplasmic binding protein CeuE complexed with a synthetic catalyst

PDB DOI: https://doi.org/10.2210/pdb5OD5/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-04 Released: 2018-08-01
Deposition Author(s): Duhme-Klair, A.K., Raines, D.J., Clarke, J.E., Blagova, E.V., Dodson, E.J., Wilson, K.S.
Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.223 (Depositor), 0.226 (DCC)
R-Value Work:
0.177 (Depositor), 0.186 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Redox-switchable siderophore anchor enables reversible artificial metalloenzyme assembly

Raines, A.D.J., Clarke, J.E., Blagova, E., Dodson, E.J., Wilson, K.S., Duhme-Klair, A.K.

(2018) Nat Catal

DOI: https://doi.org/10.1038/s41929-018-0124-3

Macromolecule Content

Total Structure Weight: 99.61 kDa
Atom Count: 7,020
Modeled Residue Count: 864
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterochelin ABC transporter substrate-binding protein	A, B, C	288	Campylobacter jejuni	Mutation(s): 0 Gene Names: AD53_07815, BKM79_06765
UniProt
Find proteins for Q0P8Q4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P8Q4 Go to UniProtKB: Q0P8Q4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0P8Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
95B Query on 95B Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C] mmCIF format, chain F [auth A] mmCIF format, chain S [auth C]	F [auth A], S [auth C]	Azotochelin C₂₀ H₂₂ N₂ O₈ KQPFLOCEYZIIRD-ZDUSSCGKSA-N		Interactions Focus chain F [auth A] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain S [auth C]
7PG Query on 7PG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL C₁₇ H₃₆ O₉ SZGNWRSFHADOMY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
RIR Query on RIR Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain H [auth A] MOL2 format, chain U [auth C] MOL2 format, chain H [auth A] mmCIF format, chain U [auth C] mmCIF format, chain H [auth A]	H [auth A], U [auth C]	[(1,2,3,4,5-Eta)-1,2,3,4,5-Pentamethylcyclopentadienyl]iridium(III) C₁₀ H₁₅ Ir VPSULBJUKFCKKU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain U [auth C]
9RT Query on 9RT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C]	G [auth A], T [auth C]	4-(aminomethyl)-~{N}-(pyridin-2-ylmethyl)benzenesulfonamide C₁₃ H₁₅ N₃ O₂ S XVNHUDOTGRKSHU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain T [auth C]
IR Query on IR Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C]	E [auth A] L [auth B] M [auth B] N [auth B] Q [auth C] E [auth A], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C]	IRIDIUM ION Ir MOHYGSBMXIJZBJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain I [auth A]	I [auth A], O [auth B], V [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain V [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	D [auth A], K [auth B], P [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223 (Depositor), 0.226 (DCC)
R-Value Work: 0.177 (Depositor), 0.186 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.692	α = 87.38
b = 62.759	β = 76.9
c = 68.195	γ = 79.27

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/L024829/1

Revision History (Full details and data files)

Version 1.0: 2018-08-01
Type: Initial release
Version 1.1: 2018-09-26
Changes: Data collection, Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations