9EQD | pdb_00009eqd

Crystal structure of an engineered enzyme containing a genetically encoded thiourea, CT1.5

PDB DOI: https://doi.org/10.2210/pdb9EQD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-21 Released: 2025-10-01
Deposition Author(s): Hardy, F.J.
Funding Organization(s): Engineering and Physical Sciences Research Council, Human Frontier Science Program (HFSP), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free:
0.190 (Depositor), 0.191 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Enzymatic photocatalysis mediated by a genetically encoded thiourea

Taylor, C.J., Hardy, F.J., Green, A.P.

To be published.

Macromolecule Content

Total Structure Weight: 28.07 kDa
Atom Count: 2,353
Modeled Residue Count: 238
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CT1.5	A	242	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain J [auth A]	B [auth A], J [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain J [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1H96 Query on A1H96	A	L-PEPTIDE LINKING	C₁₀ H₂₁ N₃ O₂ S		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.190 (Depositor), 0.191 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.919	α = 90
b = 69.919	β = 90
c = 122.243	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Hardy, F.J.

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/W524347/1
Human Frontier Science Program (HFSP)	France	RGP0004/2022
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M027023/1