4RNG | pdb_00004rng

Crystal structure of a bacterial homologue of SWEET transporters

PDB DOI: https://doi.org/10.2210/pdb4RNG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Thermodesulfovibrio yellowstonii DSM 11347
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2014-10-24 Released: 2014-11-19
Deposition Author(s): Hu, Q., Wang, J., Yan, C., Yan, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.294 (Depositor), 0.278 (DCC)
R-Value Work:
0.251 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a bacterial homologue of SWEET transporters.

Wang, J., Yan, C., Li, Y., Hirata, K., Yamamoto, M., Yan, N., Hu, Q.

(2014) Cell Res 24: 1486-1489

PubMed: 25378180 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2014.144
Primary Citation Related Structures:
4RNG

Organizational Affiliation

1] State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China [2] Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China [3] Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 66.24 kDa
Atom Count: 4,007
Modeled Residue Count: 494
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MtN3/saliva family	A, B, C, D, E A, B, C, D, E, F	94	Thermodesulfovibrio yellowstonii DSM 11347	Mutation(s): 0 Gene Names: THEYE_A1538 Membrane Entity: Yes
UniProt
Find proteins for B5YGD6 (Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)) Explore B5YGD6 Go to UniProtKB: B5YGD6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5YGD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A], N [auth E], O [auth E], Q [auth F]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain G [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain Q [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain P [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E]	H [auth A] I [auth A] J [auth B] K [auth C] L [auth D] H [auth A], I [auth A], J [auth B], K [auth C], L [auth D], M [auth D], P [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain P [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.294 (Depositor), 0.278 (DCC)
R-Value Work: 0.251 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.88	α = 90
b = 96.155	β = 90
c = 119.797	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2014-12-24
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4RNG | pdb_00004rng

Crystal structure of a bacterial homologue of SWEET transporters

Literature

Crystal structure of a bacterial homologue of SWEET transporters.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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