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- PDB-10yn: Joint X-ray/neutron structure of E53Q mutant of Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 10yn
TitleJoint X-ray/neutron structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT)
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / homodimer / pyridoxal-5'-phosphate / one-carbon metabolism / inactive mutant
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DEUTERATED WATER / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKovalevsky, A. / Drago, V.N. / Phillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: Rsc Adv / Year: 2026
Title: Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study
Authors: Drago, V.N. / Phillips, R.S. / Kovalevsky, A.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5464
Polymers89,3542
Non-polymers1922
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-95 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.819, 83.522, 95.425
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44677.031 Da / Num. of mol.: 2 / Mutation: E53Q
Source method: isolated from a genetically manipulated source
Details: LLP is the pyridoxal-5'-phosphate covalently bound to K226 in the internal aldimine form
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: glyA, TthAA11_16450 / Production host: Escherichia coli (E. coli)
References: UniProt: A0AAD1KUU5, glycine hydroxymethyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5 M lithium sulfate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D12.8 - 4.5
ROTATING ANODERIGAKU MICROMAX-007 HF21.5406
Detector
TypeIDDetectorDate
MAATEL IMAGINE1IMAGE PLATEOct 2, 2024
DECTRIS EIGER R 4M2PIXELOct 3, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
24.51
31.54061
Reflection

Entry-ID: 10YN

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.4-58.82830477.33.50.9570.1830.10113.8
1.65-95.410987399.13.80.9670.0670.039219.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
2.4-2.523.10.3012.310830.6860.171162.4
1.65-1.712.40.3612.5107730.8230.251297.1

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Processing

Software
NameVersionClassification
LAUEGENdata reduction
CrysalisProdata reduction
LSCALEdata scaling
SCALAdata scaling
Aimlessdata scaling
PHASERphasing
nCNS1.0.8refinement
Refinement

Biso max: 92.58 Å2 / Biso mean: 19.89 Å2 / Biso min: 4 Å2 / Rfactor Rfree error: 0.008 / R Free selection details: random / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used / Bsol: 22.3711 Å2 / ksol: 0.660311 e/Å3

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.4-40NEUTRON DIFFRACTION0.2630.236112022485236054.765.11
1.65-29.4X-RAY DIFFRACTION0.1970.189501493980989945.189.32
Refine analyze
Refine-ID#notag 0
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.450.42
Luzzati d res low-5
Luzzati sigma a-0.52
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.180.16
Luzzati d res low-5
Luzzati sigma a-0.15
Refine funct minimized
Refine-IDType
NEUTRON DIFFRACTIONJoint X-ray/neutron ML
X-RAY DIFFRACTIONJoint X-ray/neutron ML
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 10 505 6765
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.009
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg19
NEUTRON DIFFRACTIONx_torsion_impr_deg1.12
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg19
X-RAY DIFFRACTIONx_torsion_impr_deg1.12
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error% reflection obs (%)
2.4-2.510.3831155.60.3691925NEUTRON DIFFRACTION0.03645.4
2.51-2.640.32974.40.3692085NEUTRON DIFFRACTION0.03348.1
2.64-2.810.4121225.50.3592115NEUTRON DIFFRACTION0.03749.7
2.81-3.020.3621264.80.3312512NEUTRON DIFFRACTION0.03258.6
3.02-3.330.3551344.60.3122789NEUTRON DIFFRACTION0.03164.5
3.33-3.810.3091604.50.2893368NEUTRON DIFFRACTION0.02477.7
3.81-4.80.2951734.40.2963754NEUTRON DIFFRACTION0.02286.5
4.8-38.260.4271934.70.4273937NEUTRON DIFFRACTION0.03189.3
1.65-1.720.2584835.20.2398887X-RAY DIFFRACTION0.01267.8
1.72-1.820.2435775.30.21810304X-RAY DIFFRACTION0.0178.7
1.82-1.930.2266065.10.20411259X-RAY DIFFRACTION0.00985.9
1.93-2.080.2086284.90.19112132X-RAY DIFFRACTION0.00892.1
2.08-2.290.2036875.20.18612575X-RAY DIFFRACTION0.00895.8
2.29-2.620.1946885.10.18312762X-RAY DIFFRACTION0.00796.9
2.62-3.30.1726955.10.17412963X-RAY DIFFRACTION0.00798.2
3.3-29.40.1576504.70.16213098X-RAY DIFFRACTION0.00697.8

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