8DOQ | pdb_00008doq

Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P21 Form)

• PDB DOI: https://doi.org/10.2210/pdb8DOQ/pdb

• Classification: ISOMERASE
• Organism(s): Klebsiella aerogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-07-14 Released: 2022-07-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)

Liu, L., Seibold, S., Battaile, K.P., Lovell, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.03 kDa 
• Atom Count: 3,614 
• Modeled Residue Count: 437 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase	A, B	253	Klebsiella aerogenes	Mutation(s): 4  Gene Names: pyrF, BXQ27_18035, HV316_11080, KCTC 2190 EC: 4.1.1.23

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	C [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
MPD	D [auth A], E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38DOQ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.35	α = 90
b = 70.5	β = 90.91
c = 66.84	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-22
  Changes: Data collection