3L6U | pdb_00003l6u

Crystal structure of abc-type sugar transport system, Periplasmic component from exiguobacterium sibiricum

• PDB DOI: https://doi.org/10.2210/pdb3L6U/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Exiguobacterium artemiae 255-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-25 Released: 2010-01-12 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Crystal structure of abc-type sugar transport system, Periplasmic component from exiguobacterium sibiricum

Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.4 kDa 
• Atom Count: 4,368 
• Modeled Residue Count: 548 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-TYPE SUGAR TRANSPORT SYSTEM PERIPLASMIC COMPONENT	A, B	293	Exiguobacterium artemiae 255-15	Mutation(s): 0  Gene Names: Exig_0838
UniProt
Find proteins for B1YL86 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YL86  Go to UniProtKB:  B1YL86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.932	α = 90
b = 57.309	β = 106.7
c = 73.131	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-10-24
  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