4Z7E

Soluble binding domain of Lmo1422 ABC-transporter

PDB DOI: https://doi.org/10.2210/pdb4Z7E/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-07 Released: 2016-04-13
Deposition Author(s): Ruiz, S.J., Guskov, A., Poolman, B.
Funding Organization(s): NWO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.198
R-Value Work: 0.153
R-Value Observed: 0.155

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE

Ruiz, S.J., Schuurman-Wolters, G.K., Poolman, B.

(2016) Crystals (Basel) 6: 162

DOI: https://doi.org/10.3390/cryst6120162

Macromolecule Content

Total Structure Weight: 67.9 kDa
Atom Count: 4,949
Modelled Residue Count: 540
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo1422 protein	A, B	293	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo1422
UniProt
Find proteins for Q8Y775 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y775 Go to UniProtKB: Q8Y775
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y775
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
PPI Query on PPI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	C [auth A], D [auth A], E [auth A], H [auth B]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.198
R-Value Work: 0.153
R-Value Observed: 0.155
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 45.96	α = 90
b = 62.87	β = 91.71
c = 97.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Ruiz, S.J.

Guskov, A.

Poolman, B.

Funding Organization	Location	Grant Number
NWO	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2017-01-11
Changes: Source and taxonomy
Version 1.2: 2017-05-17
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Refinement description

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Help and Resources

4Z7E

Soluble binding domain of Lmo1422 ABC-transporter

Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)