7YUA | pdb_00007yua

Structural Insight into a Metal-Dependent Mutase MtdL Revealing an Arginine Residue Covalently Mediated Interconversion between Nucleotide-Based furanose and pyranose

PDB DOI: https://doi.org/10.2210/pdb7YUA/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Marinactinospora thermotolerans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-08-16 Released: 2023-07-26
Deposition Author(s): Chi, C.B., Ma, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.244 (Depositor), 0.246 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Insight into a Metal-Dependent Mutase Revealing an Arginine Residue-Covalently Mediated Interconversion between Nucleotide-Based Pyranose and Furanose.

Chi, C.B., Xu, R., Chen, Q.Q., Zhang, X.H., Shi, X.M., Jin, H.W., Yin, F., Jia, H.L., Zhang, L.R., Yang, D.H., Ju, J.H., Li, Q.L., Ma, M.

(2023) ACS Catal 13: 1597-1603

DOI: https://doi.org/10.1021/acscatal.2c04907

Macromolecule Content

Total Structure Weight: 168.85 kDa
Atom Count: 12,306
Modeled Residue Count: 1,488
Deposited Residue Count: 1,504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transglycosylse	A, B, C, D	376	Marinactinospora thermotolerans	Mutation(s): 0
UniProt
Find proteins for G8HX37 (Marinactinospora thermotolerans) Explore G8HX37 Go to UniProtKB: G8HX37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G8HX37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], M [auth C], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	F [auth A] G [auth A] H [auth A] J [auth B] K [auth B] F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], S [auth D], T [auth D], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]