8U99

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Serine adduct)

• PDB DOI: https://doi.org/10.2210/pdb8U99/pdb

• Classification: LIGASE
• Organism(s): Klebsiella aerogenes KCTC 2190
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-09-18 Released: 2023-09-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Serine adduct)

Liu, L., Lovell, S., Battaile, K.P., Cooper, 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: 89.25 kDa 
• Atom Count: 6,792 
• Modelled Residue Count: 782 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine beta-lyase	A, B	403	Klebsiella aerogenes KCTC 2190	Mutation(s): 2  Gene Names: EAE_03480 EC: 4.4.1.8
UniProt
Find proteins for A0A0H3FMF8 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FMF8  Go to UniProtKB:  A0A0H3FMF8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPD	E [auth A], I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SER (Subject of Investigation/LOI)	D [auth A], H [auth B]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
CL	F [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.207 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M38U99

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.814	α = 90
b = 131.172	β = 103.93
c = 82.672	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release