9IQU | pdb_00009iqu

phage HY126 dCMP hydroxylase-AfhB with sustrate dCMP

PDB DOI: https://doi.org/10.2210/pdb9IQU/pdb

Classification: HYDROLASE
Organism(s): Phage #D
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-13 Released: 2025-07-16
Deposition Author(s): Yu, H., Lianrong, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.196 (Depositor), 0.199 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

STRUCTURE OF protein XAN60475 at 1.1.96 angstroms resolution

Yu, H.

To be published.

Macromolecule Content

Total Structure Weight: 27.18 kDa
Atom Count: 2,062
Modeled Residue Count: 217
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	234	Phage #D	Mutation(s): 0 Gene Names: 308Ecol101PP_00194
UniProt
Find proteins for A0AA50FDD6 (Escherichia phage 308Ecol101PP) Explore A0AA50FDD6 Go to UniProtKB: A0AA50FDD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA50FDD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCM (Subject of Investigation/LOI) Query on DCM 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]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₇ P NCMVOABPESMRCP-SHYZEUOFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL (Subject of Investigation/LOI) Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.219 (Depositor), 0.221 (DCC)
R-Value Work: 0.196 (Depositor), 0.199 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.19	α = 90
b = 65.19	β = 90
c = 231.933	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHENIX	phasing
autoPROC	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
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.