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- PDB-9o50: Room-temperature X-ray structure of Thermus thermophilus SHMT in ... -

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Basic information

Entry
Database: PDB / ID: 9o50
TitleRoom-temperature X-ray structure of Thermus thermophilus SHMT in complex with tetrahydrofolate (THF)
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / PLP-dependent enzyme / substrate complex / internal aldimine
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-serine / 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
(6S)-5,6,7,8-TETRAHYDROFOLATE / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Febs J. / Year: 2026
Title: Neutron diffraction reveals protonation states in pyridoxal-5'-phosphate-free and glycine external aldimine-bound serine hydroxymethyltransferase.
Authors: Drago, V.N. / Blakeley, M.P. / Phillips, R.S. / Kovalevsky, A.
History
DepositionApr 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,0906
Polymers89,3562
Non-polymers7344
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-87 kcal/mol
Surface area25790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.918, 83.447, 95.294
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 44678.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 3 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM sodium acetate pH 5.5, 1M ammonium sulfate and 0.5 M lithium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→95.26 Å / Num. obs: 84515 / % possible obs: 98.9 % / Redundancy: 3.1 % / CC1/2: 0.967 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.059 / Net I/σ(I): 16.1
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8255 / CC1/2: 0.741 / Rpim(I) all: 0.309 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.45 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.175 4210 4.99 %random
Rwork0.1438 ---
obs0.1454 84322 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 47 449 6746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136515
X-RAY DIFFRACTIONf_angle_d1.2288841
X-RAY DIFFRACTIONf_dihedral_angle_d8.327946
X-RAY DIFFRACTIONf_chiral_restr0.088964
X-RAY DIFFRACTIONf_plane_restr0.0131167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.30751410.25342579X-RAY DIFFRACTION96
1.82-1.840.27471340.23682627X-RAY DIFFRACTION97
1.84-1.860.27111230.2222577X-RAY DIFFRACTION96
1.86-1.890.24581470.20272630X-RAY DIFFRACTION98
1.89-1.910.21941440.19062630X-RAY DIFFRACTION98
1.91-1.940.22991320.17562629X-RAY DIFFRACTION98
1.94-1.970.19211750.16742639X-RAY DIFFRACTION98
1.97-20.2181500.1612612X-RAY DIFFRACTION98
2-2.030.21351390.16332677X-RAY DIFFRACTION99
2.03-2.060.20261150.16022640X-RAY DIFFRACTION98
2.06-2.10.19331280.15892697X-RAY DIFFRACTION99
2.1-2.130.17931290.14882665X-RAY DIFFRACTION98
2.13-2.180.19751240.14752697X-RAY DIFFRACTION99
2.18-2.220.16041410.13492639X-RAY DIFFRACTION99
2.22-2.270.16191510.13262698X-RAY DIFFRACTION99
2.27-2.320.18121280.12732620X-RAY DIFFRACTION99
2.32-2.380.19361340.13652730X-RAY DIFFRACTION100
2.38-2.440.17341460.13342709X-RAY DIFFRACTION100
2.44-2.510.14941320.13622683X-RAY DIFFRACTION100
2.51-2.60.19241610.13572673X-RAY DIFFRACTION100
2.6-2.690.17251670.13512715X-RAY DIFFRACTION100
2.69-2.80.16031280.13572711X-RAY DIFFRACTION100
2.8-2.920.17581430.13292685X-RAY DIFFRACTION100
2.92-3.080.14681530.13132721X-RAY DIFFRACTION100
3.08-3.270.15961380.12562713X-RAY DIFFRACTION100
3.27-3.520.15891260.12592735X-RAY DIFFRACTION100
3.52-3.880.12051560.10622684X-RAY DIFFRACTION100
3.88-4.430.13111640.10722721X-RAY DIFFRACTION100
4.43-5.580.13331310.12422757X-RAY DIFFRACTION100
5.58-29.450.25171300.22032619X-RAY DIFFRACTION93

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