4PTN

Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde

PDB DOI: https://doi.org/10.2210/pdb4PTN/pdb

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

Deposited: 2014-03-11 Released: 2014-12-03
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: 0.203
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.

Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

(2008) Proteins 71: 2102-2108

PubMed: 18361457 Search on PubMed
DOI: https://doi.org/10.1002/prot.22023
Primary Citation of Related Structures:
2V8Z, 2V9D, 4PTN

Organizational Affiliation

School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamilnadu, India.

Macromolecule Content

Total Structure Weight: 149.46 kDa
Atom Count: 9,706
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 (PDB Primary Data), 4.1.2.51 (UniProt), 4.1.2.28 (UniProt)
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
GXV Query on GXV Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	G [auth A], N [auth B], T [auth C], X [auth D]	L-glyceraldehyde C₃ H₆ O₃ MNQZXJOMYWMBOU-GSVOUGTGSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Z [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth D]	P [auth B], Z [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Z [auth D] Interactions & Density Focus chain P [auth B] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], Q [auth C], R [auth C], S [auth C], V [auth D], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	H [auth A], O [auth B], U [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.203
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.2	α = 90
b = 155.07	β = 90
c = 55.4	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 2.0: 2020-07-08
Changes: Atomic model, Database references, Derived calculations, Structure summary
Version 3.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description