4OE7

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

PDB DOI: https://doi.org/10.2210/pdb4OE7/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-12 Released: 2014-12-24
Deposition Author(s): Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 151.1 kDa
Atom Count: 9,434
Modelled Residue Count: 1,192
Deposited Residue Count: 1,372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-keto-3-deoxy-galactonate aldolase YagE	A, B, C, D	343	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0268, JW0261, yagE EC: 4.1.2
UniProt
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682 Go to UniProtKB: P75682
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75682
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GXS Query on GXS Download Ideal Coordinates CCD File SDF format, chain UA [auth D] SDF format, chain Y [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain Y [auth B]	UA [auth D], Y [auth B]	(4R)-4-hydroxy-2,5-dioxopentanoic acid C₅ H₆ O₅ QZKCWTOLHHFWCD-GSVOUGTGSA-N		Interactions Focus chain UA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain UA [auth D] Focus chain Y [auth B]
GXP Query on GXP Download Ideal Coordinates CCD File SDF format, chain TA [auth D] SDF format, chain X [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain X [auth B]	TA [auth D], X [auth B]	(4S)-4-hydroxy-2,5-dioxopentanoic acid C₅ H₆ O₅ QZKCWTOLHHFWCD-VKHMYHEASA-N		Interactions Focus chain TA [auth D] Focus chain X [auth B] Interactions & Density Focus chain TA [auth D] Focus chain X [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth D]	AA [auth C], F [auth A], P [auth B], Q [auth B], QA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth D]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain N [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain N [auth A]	KA [auth C], N [auth A]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain KA [auth C] Focus chain N [auth A] Interactions & Density Focus chain KA [auth C] Focus chain N [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain R [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C]	CA [auth C] DA [auth C] E [auth A] EA [auth C] FA [auth C] CA [auth C], DA [auth C], E [auth A], EA [auth C], FA [auth C], G [auth A], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], LA [auth C], MA [auth D], NA [auth D], O [auth B], OA [auth D], PA [auth D], R [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain R [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth C]
GXT Query on GXT Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	ethanedial C₂ H₂ O₂ LEQAOMBKQFMDFZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B]	BA [auth C], H [auth A], RA [auth D], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain RA [auth D] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain RA [auth D] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.233
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.24	α = 90
b = 155.14	β = 90
c = 55.58	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations