8A9C | pdb_00008a9c

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP

• PDB DOI: https://doi.org/10.2210/pdb8A9C/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-28 Released: 2023-07-12 
• Deposition Author(s): Adam, S., Hirsch, A.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP

Adam, S., Hirsch, A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 126.96 kDa 
• Atom Count: 8,825 
• Modeled Residue Count: 1,047 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose-5-phosphate synthase	A, B	586	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  dxs_3, dxs, dxs_1, BN49_1346, FXN67_12755, GJJ18_13560, GJJ26_020415, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3649733_02709, SAMEA4364603_02966, dxs_2, DRB11_07540, SAMEA3512100_02923 EC: 2.2.1.7
UniProt
Find proteins for A6T5F3 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T5F3  Go to UniProtKB:  A6T5F3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	C [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.673	α = 90
b = 72.559	β = 108.46
c = 91.438	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Adam, S., Hirsch, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Source and taxonomy
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description