3BRS | pdb_00003brs

Crystal structure of sugar transporter from Clostridium phytofermentans

• PDB DOI: https://doi.org/10.2210/pdb3BRS/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Lachnoclostridium phytofermentans ISDg
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-02-05 
• Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Toro, R., Meyers, A.J., Wasserman, S., 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: 2.00 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of sugar transporter from Clostridium phytofermentans.

Malashkevich, V.N., Patskovsky, Y., Toro, R., Meyers, A.J., Wasserman, S., 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.66 kDa 
• Atom Count: 4,477 
• Modelled Residue Count: 542 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A, B	289	Lachnoclostridium phytofermentans ISDg	Mutation(s): 0  Gene Names: CphyDRAFT_2568
UniProt
Find proteins for A9KIC5 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Explore A9KIC5  Go to UniProtKB:  A9KIC5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.62	α = 90
b = 54.7	β = 111.78
c = 90.24	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Toro, R., Meyers, A.J., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references