5DBE

Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A

• PDB DOI: https://doi.org/10.2210/pdb5DBE/pdb
• Entry: 5DBE supersedes: 4ZU8

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Haemophilus influenzae Rd KW20, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-21 Released: 2015-09-09 
• Deposition Author(s): Singh, A.K., Kaushik, A., Ekka, M.K., Kumaran, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.227 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Crystal Structure Of O-Acetylserine Sulfhydrylase From Haemophilus Influenzae In Complex With Pre-Reactive O-Acetyl Serine, Alpha-Aminoacrylate Reactionintermediate And Peptide Inhibitor At The Resolution Of 2.25A

Singh, A.K., Kaushik, A., Ekka, M.K., Kumaran, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2,348 
• Modelled Residue Count: 312 
• Deposited Residue Count: 342 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A [auth X]	332	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: cysK, HI_1103 EC: 2.5.1.47
UniProt
Find proteins for P45040 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P45040  Go to UniProtKB:  P45040

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal peptide from Serine acetyltransferase	B [auth A]	10	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  EC: 2.3.1.30
UniProt
Find proteins for P29847 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P29847  Go to UniProtKB:  P29847

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0JO	F [auth X]	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid C11 H13 N2 O7 P BHIGINKEEFZJGX-YIXHJXPBSA-N
OAS	D [auth X]	O-ACETYLSERINE C5 H9 N O4 VZXPDPZARILFQX-BYPYZUCNSA-N
GOL	C [auth X], E [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.227 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.643	α = 90
b = 112.643	β = 90
c = 45.898	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Singh, A.K., Kaushik, A., Ekka, M.K., Kumaran, S.
• This entry supersedes: 4ZU8

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Non-polymer description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description