5DBH | pdb_00005dbh

Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate

• PDB DOI: https://doi.org/10.2210/pdb5DBH/pdb
• Entry: 5DBH supersedes: 4LHG

• Classification: TRANSFERASE
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of O-acetylserine sulfhydrylase from haemophilus influenzae in complex with reaction intermediate alpha-aminoacrylate

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

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: 34.66 kDa 
• Atom Count: 2,423 
• Modelled Residue Count: 312 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A [auth X]	322	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0JO	C [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
GOL	B [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.66	α = 90
b = 112.66	β = 90
c = 43.369	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): Kaushik, A., Ekka, M.K., Singh, A.K., Kumaran, S.
• This entry supersedes: 4LHG

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