1A0T | pdb_00001a0t

SUCROSE-SPECIFIC PORIN, WITH BOUND SUCROSE MOLECULES

PDB DOI: https://doi.org/10.2210/pdb1A0T/pdb

Classification: OUTER MEMBRANE PROTEIN
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 1997-12-08 Released: 1998-03-18
Deposition Author(s): Diederichs, K., Welte, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.246 (Depositor)
R-Value Work:
0.207 (Depositor), 0.214 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.

Forst, D., Welte, W., Wacker, T., Diederichs, K.

(1998) Nat Struct Biol 5: 37-46

PubMed: 9437428 Search on PubMed
DOI: https://doi.org/10.1038/nsb0198-37
Primary Citation Related Structures:
1A0S, 1A0T

PubMed Abstract:
The X-ray structure of a sucrose-specific porin (ScrY) from Salmonella typhimurium has been determined by multiple isomorphous replacement at 2.4 A resolution both in its uncomplexed form and with bound sucrose. ScrY is a noncrystallographic trimer of identical subunits, each with 413 structurally well-defined amino acids. A monomer is built up of 18 anti-parallel beta-strands surrounding a hydrophilic pore, with a topology closely similar to that of maltoporin. Two non-overlapping sucrose-binding sites were identified in difference Fourier maps. The higher permeability for sucrose of ScrY as compared to maltoporin is mainly accounted for by differences in their pore-lining residues.

Organizational Affiliation

Institut für Biophysik und Strahlenbiologie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.

Macromolecule Content

Total Structure Weight: 138.18 kDa
Atom Count: 10,077
Modeled Residue Count: 1,239
Deposited Residue Count: 1,239
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCROSE-SPECIFIC PORIN	A [auth P], B [auth Q], C [auth R]	413	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: SCRY Membrane Entity: Yes
UniProt
Find proteins for P22340 (Salmonella typhimurium) Explore P22340 Go to UniProtKB: P22340
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22340
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], I [auth F]	2		N/A	Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F]
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth R] SDF format, chain K [auth Q] SDF format, chain J [auth P] MOL2 format, chain L [auth R] MOL2 format, chain K [auth Q] MOL2 format, chain J [auth P] mmCIF format, chain L [auth R] mmCIF format, chain K [auth Q] mmCIF format, chain J [auth P]	J [auth P], K [auth Q], L [auth R]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth P] Focus chain K [auth Q] Focus chain L [auth R] Interactions & Density Focus chain J [auth P] Focus chain K [auth Q] Focus chain L [auth R]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	D [auth A] E [auth B] F [auth C] G [auth D] H [auth E] D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], I [auth F]	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth E] Focus chain I [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.246 (Depositor)
R-Value Work: 0.207 (Depositor), 0.214 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.8	α = 90
b = 111.8	β = 90
c = 147.8	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-03-18

Deposition Author(s):

Diederichs, K.

Welte, W.

Revision History (Full details and data files)

Version 1.0: 1998-03-18
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-02
Changes: Database references, Refinement description, Structure summary
Version 2.2: 2024-05-22
Changes: Data collection