5DB5 | pdb_00005db5

Crystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21

• PDB DOI: https://doi.org/10.2210/pdb5DB5/pdb

• Classification: TRANSFERASE, LYASE
• Organism(s): Escherichia coli DH5[alpha]
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-20 Released: 2016-08-24 
• Deposition Author(s): Arbing, M.A., Shin, A., Koo, C.W., Medrano-Soto, A., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PLP-bound E. coli SufS (cysteine persulfide intermediate) in space group P21

Arbing, M.A., Shin, A., Koo, C.W., Medrano-Soto, A., Eisenberg, D.

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: 90.13 kDa 
• Atom Count: 6,457 
• Modeled Residue Count: 809 
• Deposited Residue Count: 814 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase	A, B	407	Escherichia coli DH5[alpha]	Mutation(s): 0  Gene Names: sufS, csdB, ynhB, b1680, JW1670 EC: 2.8.1.7 (PDB Primary Data), 4.4.1.16 (PDB Primary Data), 3.13.1 (UniProt)
UniProt
Find proteins for P77444 (Escherichia coli (strain K12)) Explore P77444  Go to UniProtKB:  P77444

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CIT	H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CYS	E [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
EDO	D [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.68	α = 90
b = 114.15	β = 116.21
c = 63.11	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Arbing, M.A., Shin, A., Koo, C.W., Medrano-Soto, A., Eisenberg, D.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection