6L3E | pdb_00006l3e

Crystal structure of Salmonella enterica sugar-binding protein MalE

PDB DOI: https://doi.org/10.2210/pdb6L3E/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Salmonella enterica
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-10-10 Released: 2019-10-23
Deposition Author(s): Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of Salmonella enterica sugar-binding protein MalE

Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 42.35 kDa
Atom Count: 3,383
Modelled Residue Count: 365
Deposited Residue Count: 370
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A	370	Salmonella enterica	Mutation(s): 0 Gene Names: malE, AL463_06150, EDJ01_24875
UniProt
Find proteins for P19576 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P19576 Go to UniProtKB: P19576
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19576
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G87171PZ GlyCosmos: G87171PZ GlyGen: G87171PZ

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
MPD (Subject of Investigation/LOI) Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
2ME (Subject of Investigation/LOI) Query on 2ME Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	METHOXYETHANE C₃ H₈ O XOBKSJJDNFUZPF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010 Query on PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.714	α = 90
b = 89.692	β = 114.766
c = 64.066	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History (Full details and data files)

Version 1.0: 2019-10-23
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-27
Changes: Data collection, Database references, Structure summary

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Crystal structure of Salmonella enterica sugar-binding protein MalE

The crystal structure of Salmonella enterica sugar-binding protein MalE

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources