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- PDB-32jn: Structure of the pathogenic variant P157S of Human SHMT2 in the a... -

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Basic information

Entry
Database: PDB / ID: 32jn
TitleStructure of the pathogenic variant P157S of Human SHMT2 in the apo open dimeric conformation
ComponentsSerine 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: 2.658 Å
AuthorsGiardina, G. / Boumis, G. / Di Matteo, A. / Breccia, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)MX-2363European 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 13, 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: Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)53,7991
Polymers53,7991
Non-polymers00
Water70339
1
A: Serine hydroxymethyltransferase, mitochondrial

A: Serine hydroxymethyltransferase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)107,5982
Polymers107,5982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5160 Å2
ΔGint-27 kcal/mol
Surface area33520 Å2
Unit cell
Length a, b, c (Å)94.716, 74.153, 74.349
Angle α, β, γ (deg.)90.00, 108.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 53799.059 Da / Num. of mol.: 1 / Mutation: P157S
Source method: isolated from a genetically manipulated source
Details: crystallized construct: SHMT2 Isoform 3 differences from canonical isoform: 1-21 missing and additional residues (GSH) at the N-ter belonging to cleaved His-tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: MoORPHEUS screen (Molecular Dimensions) condition F9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0596 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0596 Å / Relative weight: 1
ReflectionResolution: 2.658→57.2 Å / Num. obs: 13465 / % possible obs: 95.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 65.19 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.9
Reflection shellResolution: 2.658→2.704 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 501 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimless0.7.7data scaling
XDSFeb 5, 2021 (BUILT 20210323)data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.658→57.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.65 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26411 651 4.8 %RANDOM
Rwork0.20538 ---
obs0.20829 12814 95.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.774 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å22.67 Å2
2--1.03 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.658→57.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 0 39 3289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163124
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.6544504
X-RAY DIFFRACTIONr_angle_other_deg0.421.5717140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.239534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29410515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
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_it4.9257.9441718
X-RAY DIFFRACTIONr_mcbond_other4.9257.9441718
X-RAY DIFFRACTIONr_mcangle_it7.58514.2952144
X-RAY DIFFRACTIONr_mcangle_other7.58314.2952145
X-RAY DIFFRACTIONr_scbond_it5.7888.4481603
X-RAY DIFFRACTIONr_scbond_other5.7868.4481604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.31915.3192361
X-RAY DIFFRACTIONr_long_range_B_refined13.5574.273735
X-RAY DIFFRACTIONr_long_range_B_other13.54974.293736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.658→2.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 35 -
Rwork0.417 732 -
obs--72.98 %

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