8XIY | pdb_00008xiy

Crystal structure of an omega-transaminase mutant I77L/Q97E/H210N/N245D from Aspergillus terreus in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb8XIY/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus terreus NIH2624
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-12-20 Released: 2024-02-07
Deposition Author(s): Lu, Z.Y., Hu, D., Xu, D.Z., He, Y.C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.216 (Depositor), 0.218 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Efficient bioamination with an omega-transaminase mutant from Aspergillus terreus

He, Y.C.

To be published.

Macromolecule Content

Total Structure Weight: 75.25 kDa
Atom Count: 5,515
Modeled Residue Count: 638
Deposited Residue Count: 670
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-aminoacid aminotransferase-like PLP-dependent enzyme	A, B	335	Aspergillus terreus NIH2624	Mutation(s): 4 Gene Names: ATEG_10023
UniProt
Find proteins for Q0C8G1 (Aspergillus terreus (strain NIH 2624 / FGSC A1156)) Explore Q0C8G1 Go to UniProtKB: Q0C8G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0C8G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.216 (Depositor), 0.218 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.42	α = 90
b = 135.79	β = 90
c = 116.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
AMPLE	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21978072

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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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.