5FT8 | pdb_00005ft8

Crystal structure of the complex between the cysteine desulfurase CsdA and the sulfur-acceptor CsdE in the persulfurated state at 2.50 Angstroem resolution

• PDB DOI: https://doi.org/10.2210/pdb5FT8/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-11 Released: 2016-11-23 
• Deposition Author(s): Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, F., Round, A., Campos-Oliva, R., Bruix, M., Coll, M., Tunon, I., Jimenez-Barbero, J., Vega, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.254 (Depositor) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Models: experimental

Literature

Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System

Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, F., Quintana, J.F., Round, A., Campos-Oliva, R., Bruix, M., Coll, M., Tunon, I., Jimenez-Barbero, J., Vega, M.C.

(2016) ACS Catal 6: 3975

• DOI: https://doi.org/10.1021/ACSCATAL.6B00360

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 491.42 kDa 
• Atom Count: 34,325 
• Modeled Residue Count: 4,296 
• Deposited Residue Count: 4,456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase CsdA	A, C, E, G, I, K, M, O	403	Escherichia coli K-12	Mutation(s): 0  Gene Names: csdA, ygdJ, b2810, JW2781 EC: 2.8.1.7 (PDB Primary Data), 3.13.1 (PDB Primary Data), 4.4.1.16 (PDB Primary Data)
UniProt
Find proteins for Q46925 (Escherichia coli (strain K12)) Explore Q46925  Go to UniProtKB:  Q46925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfur acceptor protein CsdE	B [auth Q], D [auth S], F [auth U], H [auth W], J [auth Y], L [auth a], N [auth c], P [auth e]	154	Escherichia coli K-12	Mutation(s): 0  Gene Names: csdE, ygdK, b2811, JW2782
UniProt
Find proteins for P0AGF2 (Escherichia coli (strain K12)) Explore P0AGF2  Go to UniProtKB:  P0AGF2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	AB [auth E], BC [auth I], IC [auth K], KA [auth C], KC [auth M], MC [auth O], Q [auth A], QB [auth G]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG	BB [auth E], CB [auth E], CC [auth I], DB [auth E], EB [auth E], GA [auth Q], JC [auth K], LA [auth C], MA [auth C], NA [auth C], OA [auth C], R [auth A], RB [auth G], S [auth A], T [auth A], ZB [auth W]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	AA [auth A], AC [auth W], BA [auth A], CA [auth A], DA [auth A], DC [auth I], EA [auth A], EC [auth I], FA [auth A], FB [auth E], FC [auth I], GB [auth E], GC [auth I], HA [auth Q], HB [auth E], HC [auth I], IA [auth Q], IB [auth E], JA [auth Q], JB [auth E], KB [auth E], LB [auth E], LC [auth M], MB [auth E], NB [auth E], OB [auth E], PA [auth C], PB [auth E], QA [auth C], RA [auth C], SA [auth C], SB [auth G], TA [auth C], TB [auth G], U [auth A], UA [auth C], UB [auth G], V [auth A], VA [auth C], VB [auth G], W [auth A], WA [auth C], WB [auth G], X [auth A], XA [auth C], XB [auth G], Y [auth A], YA [auth C], YB [auth G], Z [auth A], ZA [auth S]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, C, E, G, I, K, M, O	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.254 (Depositor) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.863	α = 90
b = 115.135	β = 90
c = 604.966	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, F., Round, A., Campos-Oliva, R., Bruix, M., Coll, M., Tunon, I., Jimenez-Barbero, J., Vega, M.C.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2019-01-02
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description