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- PDB-9rwd: High-resolution structure of human SHMT2 with covalently bound PL... -

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Basic information

Entry
Database: PDB / ID: 9rwd
TitleHigh-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE / tetrahydrofolate / one-carbon metabolism / cancer therapy target
Function / homology
Function and homology information


BRISC complex / formate biosynthetic process / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity ...BRISC complex / formate biosynthetic process / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / amino acid binding / mitochondrial nucleoid / RHOG GTPase cycle / one-carbon metabolic process / Mitochondrial protein degradation / protein tetramerization / pyridoxal phosphate binding / microtubule cytoskeleton / 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
DI(HYDROXYETHYL)ETHER / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWarlich, A. / Ruszkowski, M. / Nawrot, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2023/50/E/NZ7/00501 Poland
CitationJournal: To Be Published
Title: High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
Authors: Warlich, A. / Ruszkowski, M. / Nawrot, D.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: 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, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
C: Serine hydroxymethyltransferase, mitochondrial
D: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,26128
Polymers211,7804
Non-polymers1,48124
Water38,0662113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.184, 125.571, 135.137
Angle α, β, γ (deg.)90.000, 93.675, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 52944.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 2137 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2113 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 70 mM Tris pH 8.5, 4.375% PEG 2000, 4.375% PEG 3350, 4.375% PEG 4000, 4.375% PEG methyl ether 5000, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 1.3→80 Å / Num. obs: 469350 / % possible obs: 97.7 % / Redundancy: 6.67 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Net I/σ(I): 17.9
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 68295 / CC1/2: 0.611 / Rrim(I) all: 0.902 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→59.06 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1782 1000 0.21 %
Rwork0.1452 468306 -
obs0.1452 469306 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.08 Å2
Refinement stepCycle: LAST / Resolution: 1.3→59.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14273 0 94 2113 16480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004514703
X-RAY DIFFRACTIONf_angle_d0.830619873
X-RAY DIFFRACTIONf_chiral_restr0.0712181
X-RAY DIFFRACTIONf_plane_restr0.00822601
X-RAY DIFFRACTIONf_dihedral_angle_d12.50365517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.370.31171260.264258977X-RAY DIFFRACTION86.31
1.37-1.460.25381460.19268301X-RAY DIFFRACTION99.91
1.46-1.570.19181450.14968045X-RAY DIFFRACTION99.45
1.57-1.730.17521450.128867730X-RAY DIFFRACTION99.02
1.73-1.970.14131460.123468408X-RAY DIFFRACTION99.9
1.97-2.490.18791460.139968091X-RAY DIFFRACTION99.29
2.49-59.060.16381460.139968754X-RAY DIFFRACTION99.66

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