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- PDB-32ja: Structure of the pathogenic variant T186R of Human SHMT2 in the a... -

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Basic information

Entry
Database: PDB / ID: 32ja
TitleStructure of the pathogenic variant T186R of Human SHMT2 in the apo open dimeric conformation
ComponentsIsoform 3 of Serine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE
Function / homology
Function and homology information


formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process ...formate biosynthetic process / hydroxytrimethyllysine aldolase activity / BRISC complex / glycine metabolic process / L-allo-threonine aldolase activity / response to vitamin B6 / regulation of mitochondrial translation / regulation of oxidative phosphorylation / L-serine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / : / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / tetrahydrofolate interconversion / protein K63-linked deubiquitination / regulation of aerobic respiration / amino acid binding / RHOG GTPase cycle / mitochondrial nucleoid / one-carbon metabolic process / Mitochondrial protein degradation / protein tetramerization / pyridoxal phosphate binding / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm
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
Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGiardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission20205534European Union
CitationJournal: To Be Published
Title: Structural and functional defects of mitochondrial serine hydroxymethyltransferase genetic variants responsible for a novel neurodevelopmental syndrome
Authors: Giardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
History
DepositionJul 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)53,8651
Polymers53,8651
Non-polymers00
Water48627
1
A: Isoform 3 of Serine hydroxymethyltransferase, mitochondrial

A: Isoform 3 of Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)107,7302
Polymers107,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5410 Å2
ΔGint-20 kcal/mol
Surface area33610 Å2
Unit cell
Length a, b, c (Å)94.532, 74.469, 75.002
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isoform 3 of Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 53865.184 Da / Num. of mol.: 1 / Mutation: T186R
Source method: isolated from a genetically manipulated source
Details: Differences from canonical 1-21: Missing / Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Variant: T186R / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: MORPHUES screen (Molecular Dimensions), condition E5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→57.28 Å / Num. obs: 23332 / % possible obs: 93 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Χ2: 0.77 / Net I/σ(I): 12 / Num. measured all: 147730
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 59.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.529 / Num. measured all: 6722 / Num. unique obs: 1274 / CC1/2: 0.913 / Rpim(I) all: 0.252 / Rrim(I) all: 0.589 / Χ2: 0.97 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.164 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23175 1125 4.8 %RANDOM
Rwork0.20542 ---
obs0.20675 22205 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.173 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å22.04 Å2
2--1.17 Å2-0 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 0 27 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123313
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163158
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.8294488
X-RAY DIFFRACTIONr_angle_other_deg0.511.7627230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.406534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49510540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.715.3211693
X-RAY DIFFRACTIONr_mcbond_other4.715.3211693
X-RAY DIFFRACTIONr_mcangle_it6.6469.5562111
X-RAY DIFFRACTIONr_mcangle_other6.6449.5552112
X-RAY DIFFRACTIONr_scbond_it5.3555.8881620
X-RAY DIFFRACTIONr_scbond_other5.3535.8881621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.16210.5832378
X-RAY DIFFRACTIONr_long_range_B_refined9.67649.353567
X-RAY DIFFRACTIONr_long_range_B_other9.67549.353568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 34 -
Rwork0.297 1029 -
obs--58.12 %

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