3LV9 | pdb_00003lv9

Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb3LV9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-19 Released: 2010-03-09 
• Deposition Author(s): Nocek, B., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630

Nocek, B., Tesar, C., Cobb, G., Joachimiak, A., MCSG

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.41 kDa 
• Atom Count: 1,074 
• Modeled Residue Count: 130 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transporter	A	148	Clostridioides difficile 630	Mutation(s): 0
UniProt
Find proteins for Q183U2 (Clostridioides difficile (strain 630)) Explore Q183U2  Go to UniProtKB:  Q183U2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.641	α = 90
b = 43.641	β = 90
c = 127.763	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
MLPHARE	phasing
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Nocek, B., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary