3L49 | pdb_00003l49

CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER SUBUNIT FROM Rhodobacter sphaeroides 2.4.1

• PDB DOI: https://doi.org/10.2210/pdb3L49/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-18 Released: 2010-01-05 
• Deposition Author(s): Patskovsky, Y., Ozyurt, S., Dickey, M., Do, J., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

CRYSTAL STRUCTURE OF ABC SUGAR TRANSPORTER FROM Rhodobacter sphaeroides

Patskovsky, Y., Ozyurt, S., Dickey, M., Do, J., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 126.13 kDa 
• Atom Count: 8,872 
• Modeled Residue Count: 1,128 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC sugar (Ribose) transporter, periplasmic substrate-binding subunit	A, B, C, D	291	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RHOS4_09560, RSP_2365
UniProt
Find proteins for Q3J3W0 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J3W0  Go to UniProtKB:  Q3J3W0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	E [auth A], F [auth B], G [auth C], H [auth D]	Unknown ligand

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.31	α = 106.41
b = 75.712	β = 115.49
c = 77.438	γ = 96.71

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-05 
Deposition Author(s): Patskovsky, Y., Ozyurt, S., Dickey, M., Do, J., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary