9J32 | pdb_00009j32

Crystal structure of aminotransferase-like protein from Variovorax paradoxus mutant N174K

PDB DOI: https://doi.org/10.2210/pdb9J32/pdb

Classification: TRANSFERASE
Organism(s): Variovorax paradoxus B4
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-08-07 Released: 2025-01-29
Deposition Author(s): Ilyasov, I.O., Minyaev, M.E., Rakitina, T.V., Bakunova, A.K., Matyuta, I.O., Popov, V.O., Bezsudnova, E.Y., Boyko, K.M.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.269 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.200 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Literature

Protein of unknown function from variovorax paradoxus with amino acid substitution n174k is able to form schiff base with plp molecule

Ilyasov, I., Minyaev, M., Rakitina, T., Bakunova, A., Popov, V., Bezsudnova, E., Boyko, K.

(2024) Кристаллография 69: 981-986

DOI: https://doi.org/10.31857/S0023476124060075

Macromolecule Content

Total Structure Weight: 102.63 kDa
Atom Count: 6,973
Modeled Residue Count: 902
Deposited Residue Count: 951
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class 4	A, B, C	317	Variovorax paradoxus B4	Mutation(s): 1 Gene Names: VAPA_1c54540 EC: 2.6.1.42
UniProt
Find proteins for T1XIY1 (Variovorax paradoxus B4) Explore T1XIY1 Go to UniProtKB: T1XIY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T1XIY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.269 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.200 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.245	α = 90
b = 87.34	β = 99.45
c = 104.655	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Bezsudnova, E.Y.

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	075-15-2021-1354

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release
Version 1.1: 2025-02-05
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.