8ONM | pdb_00008onm

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with D-glutamate

PDB DOI: https://doi.org/10.2210/pdb8ONM/pdb

Classification: TRANSFERASE
Organism(s): Aminobacterium colombiense
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-03 Released: 2024-04-10
Deposition Author(s): Matyuta, I.O., Boyko, K.M., Minyaev, M.E., Shilova, S.A., Bezsudnova, E.Y., Popov, V.O.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.250 (Depositor), 0.255 (DCC)
R-Value Work:
0.195 (Depositor), 0.204 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Probing of the structural and catalytic roles of the residues in the active site of transaminase from Aminobacterium colombiense

Shilova, S.A., Khrenova, M.G., Matyuta, I.O., Nikolaeva, A.Y., Klyachko, N.L., Minyaev, M.E., Boyko, K.M., Popov, V.O., Bezsudnova, E.Y.

To be published.

Macromolecule Content

Total Structure Weight: 63.21 kDa
Atom Count: 4,774
Modeled Residue Count: 551
Deposited Residue Count: 554
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class IV	A, B	277	Aminobacterium colombiense	Mutation(s): 1 Gene Names: Amico_1844
UniProt
Find proteins for D5EHC5 (Aminobacterium colombiense (strain DSM 12261 / ALA-1)) Explore D5EHC5 Go to UniProtKB: D5EHC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5EHC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PW0 (Subject of Investigation/LOI) Query on PW0 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid C₁₃ H₁₇ N₂ O₉ P AQYBBWUPMNWMHD-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
PMP (Subject of Investigation/LOI) Query on PMP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B]	C [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], L [auth B], M [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B]