6SSD | pdb_00006ssd

Transaminase with PLP bound

PDB DOI: https://doi.org/10.2210/pdb6SSD/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces kaniharaensis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-09-06 Released: 2020-01-15
Deposition Author(s): Naismith, J.H., Gao, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.18 Å
R-Value Free:
0.129 (Depositor), 0.154 (DCC)
R-Value Work:
0.111 (Depositor)
R-Value Observed:
0.112 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6SSD

Ligand Structure Quality Assessment

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

Literature

PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.

Gao, S., Liu, H., de Crecy-Lagard, V., Zhu, W., Richards, N.G.J., Naismith, J.H.

(2019) Chem Commun (Camb) 55: 14502-14505

PubMed: 31730149 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/c9cc06975e
Primary Citation Related Structures:
6SSD, 6SSE, 6SSF, 6SSG

PubMed Abstract:
ForI is a PLP-dependent enzyme from the biosynthetic pathway of the C-nucleoside antibiotic formycin. Cycloserine is thought to inhibit PLP-dependent enzymes by irreversibly forming a PMP-isoxazole. We now report that ForI forms novel PMP-diketopiperazine derivatives following incubation with both d and l cycloserine. This unexpected result suggests chemical diversity in the chemistry of cycloserine inhibition.

Organizational Affiliation

Research Complex at Harwell, Didcot, OX11 0FA, UK.

Macromolecule Content

Total Structure Weight: 44.9 kDa
Atom Count: 4,050
Modeled Residue Count: 424
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ForI-PLP	A	424	Streptomyces kaniharaensis	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFW1 (Streptomyces kaniharaensis) Explore A0A6I8WFW1 Go to UniProtKB: A0A6I8WFW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6I8WFW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.18 Å
R-Value Free: 0.129 (Depositor), 0.154 (DCC)
R-Value Work: 0.111 (Depositor)
R-Value Observed: 0.112 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.3	α = 90
b = 92.3	β = 90
c = 118.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.