10YN | pdb_000010yn

Joint X-ray/neutron structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT)

PDB DOI: https://doi.org/10.2210/pdb10YN/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-02-12 Released: 2026-05-20
Deposition Author(s): Kovalevsky, A., Drago, V.N., Phillips, R.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.197 (Depositor), 0.342 (DCC)
R-Value Work:
0.189 (Depositor), 0.342 (DCC)

Method: NEUTRON DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.263 (Depositor)
R-Value Work:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Drago, V.N., Phillips, R.S., Kovalevsky, A.

(2026) RSC Adv 16

DOI: https://doi.org/10.1039/D6RA01814A

Macromolecule Content

Total Structure Weight: 89.55 kDa
Atom Count: 6,765
Modeled Residue Count: 804
Deposited Residue Count: 810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	405	Thermus thermophilus	Mutation(s): 1 Gene Names: glyA, TthAA11_16450 EC: 2.1.2.1
UniProt
Find proteins for A0AAD1KUU5 (Thermus thermophilus) Explore A0AAD1KUU5 Go to UniProtKB: A0AAD1KUU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAD1KUU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.197 (Depositor), 0.342 (DCC)
R-Value Work: 0.189 (Depositor), 0.342 (DCC)

Method: NEUTRON DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263 (Depositor)
R-Value Work: 0.236 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.819	α = 90
b = 83.522	β = 91.64
c = 95.425	γ = 90

Software Package:

Software Name	Purpose
LAUEGEN	data reduction
CrysalisPro	data reduction
LSCALE	data scaling
SCALA	data scaling
Aimless	data scaling
PHASER	phasing
nCNS	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM137008

Revision History (Full details and data files)

Version 1.0: 2026-05-20
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.