6VOQ | pdb_00006voq

Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6VOQ/pdb

• Classification: LYASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-31 Released: 2020-02-19 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., McChesney, C., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 22.81 kDa 
• Atom Count: 1,754 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldolase	A	207	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  fucA_2, fucA_1, fucA_3, BL124_00025510, C3483_13535, C3F39_01215, C7V41_22435, CWN54_08000, DD581_15345, DM059_14180, EAO17_27025, EXT45_05660, FAM48_01070, FAQ72_03260, FAQ97_05405, FAS39_03255, FNY87_25290, NCTC11679_02859, NCTC13465_01855, NCTC1936_02659, NCTC5047_00576, NCTC9140_04285, NCTC9601_02686, NCTC9645_06176, NCTC9661_03377, PMK1_03924, SAMEA24002668_05560, SAMEA4364603_02467, SK89_00182 EC: 4.1.2.17 (PDB Primary Data), 4.1.1.104 (UniProt)
UniProt
Find proteins for Q0QC76 (Klebsiella pneumoniae) Explore Q0QC76  Go to UniProtKB:  Q0QC76

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.436	α = 90
b = 76.436	β = 90
c = 181.682	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Stogios, P.J., Evdokimova, E., McChesney, C., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description