5WT6 | pdb_00005wt6

Cysteine persulfide intermediate of NifS from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb5WT6/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-09 Released: 2017-12-13 
• Deposition Author(s): Fujishiro, T., Nakamura, R., Takahashi, Y.
• Funding Organization(s): JSPS, the Sumitomo Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structural snapshot of cysteine desulfurase NifS with L-cysteine in initiation of catalysis

Fujishiro, T., Nakamura, R., Takahashi, Y.

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: 44.57 kDa 
• Atom Count: 2,864 
• Modeled Residue Count: 366 
• Deposited Residue Count: 401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase IscS	A	401	Helicobacter pylori 26695	Mutation(s): 2  Gene Names: iscS, HP_0220 EC: 2.8.1.7
UniProt
Find proteins for O25008 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25008  Go to UniProtKB:  O25008

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDA	D [auth A]	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID C11 H17 N2 O7 P WACJCHFWJNNBPR-ZETCQYMHSA-N
IPA	B [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.75	α = 90
b = 102.75	β = 90
c = 131.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Fujishiro, T., Nakamura, R., Takahashi, Y.

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Funding Organization	Location	Grant Number
JSPS	Japan	15H04472
JSPS	Japan	15H06085
the Sumitomo Foundation	Japan	163037

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary