7Q30 | pdb_00007q30

Mutant T91A of uridine phosphorylase from Shewanella oneidensis

PDB DOI: https://doi.org/10.2210/pdb7Q30/pdb

Classification: TRANSFERASE
Organism(s): Shewanella oneidensis MR-1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-26 Released: 2022-04-06
Deposition Author(s): Polyakov, K., Safonova, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.211 (Depositor), 0.212 (DCC)
R-Value Work:
0.157 (Depositor), 0.159 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Role of Conformational Changes of Hexameric Bacterial Uridine Phosphorylases in Substrate Binding

Polyakov, K.P., Mordkovich, N.N., Safonova, T.N., Antipov, A.N., Okorokova, N.A., Dorovatovskii, P.V., Veiko, V.P.

(2021) Crystallogr Rep 66: 786-790

DOI: https://doi.org/10.1134/S1063774521050199

Macromolecule Content

Total Structure Weight: 54.38 kDa
Atom Count: 3,940
Modeled Residue Count: 483
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A [auth DDD], B [auth AAA]	251	Shewanella oneidensis MR-1	Mutation(s): 1 Gene Names: udp, SO_4133 EC: 2.4.2.3
UniProt
Find proteins for Q8E9X9 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E9X9 Go to UniProtKB: Q8E9X9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E9X9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth DDD] SDF format, chain F [auth DDD] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain J [auth AAA] SDF format, chain G [auth DDD] MOL2 format, chain E [auth DDD] MOL2 format, chain F [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain G [auth DDD] mmCIF format, chain E [auth DDD] mmCIF format, chain F [auth DDD] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain G [auth DDD]	E [auth DDD] F [auth DDD] G [auth DDD] J [auth AAA] K [auth AAA] E [auth DDD], F [auth DDD], G [auth DDD], J [auth AAA], K [auth AAA], L [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth DDD] Focus chain F [auth DDD] Focus chain G [auth DDD] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain E [auth DDD] Focus chain F [auth DDD] Focus chain G [auth DDD] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth DDD] SDF format, chain D [auth DDD] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] MOL2 format, chain C [auth DDD] MOL2 format, chain D [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain C [auth DDD] mmCIF format, chain D [auth DDD] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA]	C [auth DDD], D [auth DDD], H [auth AAA], I [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth DDD] Focus chain D [auth DDD] Focus chain H [auth AAA] Focus chain I [auth AAA] Interactions & Density Focus chain C [auth DDD] Focus chain D [auth DDD] Focus chain H [auth AAA] Focus chain I [auth AAA]
LI (Subject of Investigation/LOI) Query on LI Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] MOL2 format, chain M [auth AAA] mmCIF format, chain M [auth AAA]	M [auth AAA]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain M [auth AAA] Interactions & Density Focus chain M [auth AAA]