9K35 | pdb_00009k35

Crystal structure of a (R)-selective transaminase (RTA) from Sphingopyxis sp.

PDB DOI: https://doi.org/10.2210/pdb9K35/pdb

Classification: TRANSFERASE
Organism(s): Sphingopyxis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-18 Released: 2025-10-22
Deposition Author(s): Qin, F.Y., Lee, K.M., Wong, K.B., Lee, K.H.
Funding Organization(s): The University Grants Committee, Research Grants Council (RGC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Expanding the substrate scope of an (R)-selective transaminase for bulky aromatic ketones through structure-guided manipulation of hydrophobic interactions.

Qin, F.Y., Lee, K.M., Wong, K.B., Lee, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 36.32 kDa
Atom Count: 2,664
Modeled Residue Count: 318
Deposited Residue Count: 323
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(R)-selective transaminase	A	323	Sphingopyxis	Mutation(s): 0
UniProt
Find proteins for Q0C8G1 (Aspergillus terreus (strain NIH 2624 / FGSC A1156)) Explore Q0C8G1 Go to UniProtKB: Q0C8G1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0C8G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.193 (Depositor), 0.193 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.951	α = 90
b = 192.951	β = 90
c = 192.951	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	C4041-18E
Other government	Hong Kong	ITS/424/18FX

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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.