4XF5 | pdb_00004xf5

Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound (S)-(+)-2-Amino-1-propanol.

• PDB DOI: https://doi.org/10.2210/pdb4XF5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Chromohalobacter israelensis DSM 3043
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-26 Released: 2015-01-28 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a TRAP periplasmic solute binding protein from Chromohalobacter salexigens DSM 3043 (Csal_0678), Target EFI-501078, with bound (S)-(+)-2-Amino-1-propanol.

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 79.77 kDa 
• Atom Count: 5,686 
• Modeled Residue Count: 634 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine translocation pathway signal	A, B	347	Chromohalobacter israelensis DSM 3043	Mutation(s): 0  Gene Names: Csal_0678
UniProt
Find proteins for Q1QZR9 (Chromohalobacter israelensis (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QZR9  Go to UniProtKB:  Q1QZR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2A1	E [auth A], H [auth B]	(2S)-2-aminopropan-1-ol C3 H9 N O BKMMTJMQCTUHRP-VKHMYHEASA-N
CL	C [auth A], D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.605	α = 90
b = 51.154	β = 115.96
c = 111.943	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Experimental preparation
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection