4U4M

Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate

PDB DOI: https://doi.org/10.2210/pdb4U4M/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-24 Released: 2015-07-29
Deposition Author(s): Manoj Kumar, P., Bhaskar, V., Manicka, S., Krishnaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate

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

To be published.

Macromolecule Content

Total Structure Weight: 130.05 kDa
Atom Count: 9,150
Modelled Residue Count: 1,192
Deposited Residue Count: 1,192
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YagE	A, B, C, D	298	Escherichia coli K-12	Mutation(s): 0 Gene Names: YAGE EC: 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 LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	H [auth A], Q [auth B], V [auth C], Y [auth D]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] I [auth A] J [auth A] K [auth A] AA [auth D], BA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth D]
URE Query on URE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	E [auth A] F [auth A] G [auth A] M [auth B] N [auth B] E [auth A], F [auth A], G [auth A], M [auth B], N [auth B], O [auth B], P [auth B], U [auth C], W [auth D], X [auth D]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.243 (Depositor), 0.240 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.4	α = 90
b = 155.64	β = 90
c = 55.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-20
Changes: Structure summary