8I07

Crystal structure of Escherichia coli glyoxylate carboligase double mutant in complex with glycolaldehyde

PDB DOI: https://doi.org/10.2210/pdb8I07/pdb

Classification: LIGASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-01-10 Released: 2023-11-22
Deposition Author(s): Kim, J.H., Kim, J.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.242
R-Value Work: 0.208
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose

Kim, J.H., Cheon, H., Jo, H.J., Kim, J.W., Kim, G.Y., Seo, H.R., Seo, P.W., Kim, J.S., Park, J.B.

(2023) Int J Biol Macromol 253: 127674

DOI: https://doi.org/10.1016/j.ijbiomac.2023.127674

Macromolecule Content

Total Structure Weight: 399.96 kDa
Atom Count: 30,814
Modelled Residue Count: 3,564
Deposited Residue Count: 3,564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate carboligase	A, B, C, D, E A, B, C, D, E, F	594	Escherichia coli K-12	Mutation(s): 2 Gene Names: gcl, b0507, JW0495 EC: 4.1.1.47
UniProt
Find proteins for P0AEP7 (Escherichia coli (strain K12)) Explore P0AEP7 Go to UniProtKB: P0AEP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth E] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain DA [auth D] SDF format, chain QA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain QA [auth F]	DA [auth D] I [auth A] KA [auth E] P [auth B] QA [auth F] DA [auth D], I [auth A], KA [auth E], P [auth B], QA [auth F], V [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain KA [auth E] Focus chain P [auth B] Focus chain QA [auth F] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain KA [auth E] Focus chain P [auth B] Focus chain QA [auth F] Focus chain V [auth C]
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain LA [auth E] SDF format, chain Q [auth B] SDF format, chain RA [auth F] SDF format, chain W [auth C] SDF format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain EA [auth D]	EA [auth D] J [auth A] LA [auth E] Q [auth B] RA [auth F] EA [auth D], J [auth A], LA [auth E], Q [auth B], RA [auth F], W [auth C]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain W [auth C]
UQ1 (Subject of Investigation/LOI) Query on UQ1 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth B]	AA [auth C] BA [auth C] HA [auth D] IA [auth D] L [auth A] AA [auth C], BA [auth C], HA [auth D], IA [auth D], L [auth A], M [auth A], MA [auth E], NA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F]
DW3 (Subject of Investigation/LOI) Query on DW3 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	FA [auth D] GA [auth D] K [auth A] R [auth B] X [auth C] FA [auth D], GA [auth D], K [auth A], R [auth B], X [auth C], Y [auth C]	2-oxidanylethanal C₂ H₄ O₂ WGCNASOHLSPBMP-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain JA [auth E] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth C] SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain OA [auth F] SDF format, chain PA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F]	CA [auth D] G [auth A] H [auth A] JA [auth E] N [auth B] CA [auth D], G [auth A], H [auth A], JA [auth E], N [auth B], O [auth B], OA [auth F], PA [auth F], U [auth C], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain U [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain U [auth C] Focus chain Z [auth C]