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- PDB-6smw: A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) i... -

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Basic information

Entry
Database: PDB / ID: 6smw
TitleA. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with pemetrexed
ComponentsSerine hydroxymethyltransferase 2, mitochondrial
KeywordsTRANSFERASE / SHMT / antifolate
Function / homology
Function and homology information


glycine metabolic process / L-serine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / plastid / pyridoxal phosphate binding / mitochondrion / zinc ion binding
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LYA / PYRIDOXAL-5'-PHOSPHATE / Chem-PLS / SERINE / Serine hydroxymethyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRuszkowski, M. / Sekula, B. / Dauter, Z.
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Contestabile, R. / Nogues, I. / Angelaccio, S. / Szczepaniak, A. / Dauter, Z.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase 2, mitochondrial
B: Serine hydroxymethyltransferase 2, mitochondrial
C: Serine hydroxymethyltransferase 2, mitochondrial
D: Serine hydroxymethyltransferase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,18250
Polymers214,1804
Non-polymers5,00246
Water34,8771936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34400 Å2
ΔGint-23 kcal/mol
Surface area63500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.899, 130.288, 150.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine hydroxymethyltransferase 2, mitochondrial / AtSHMT2 / Glycine hydroxymethyltransferase 2 / Serine methylase 2


Mass: 53545.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM2, SHMT2, At5g26780, F2P16.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: Q94C74, glycine hydroxymethyltransferase

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Non-polymers , 6 types, 1982 molecules

#2: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H17N2O8P
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-LYA / 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID / LY231514


Mass: 427.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H21N5O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#6: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1936 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The AtSHMT2 crystals were grown by vapor diffusion method in hanging drops containing 3 uL of the protein solution and 2 uL of reservoir solution. The reservoir solution was composed of 90% ...Details: The AtSHMT2 crystals were grown by vapor diffusion method in hanging drops containing 3 uL of the protein solution and 2 uL of reservoir solution. The reservoir solution was composed of 90% Hampton Research Index F8 condition (0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, and 25% polyethylene glycol 3350). Mature crystals were transferred to drops with the original screen conditions supplemented with 20% ethylene glycol, 50 mM L-serine, and 10 mM PTX. After 24-h incubation, crystals were harvested and vitrified in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→80 Å / Num. obs: 330027 / % possible obs: 99.7 % / Redundancy: 8.1 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.088 / Net I/σ(I): 18.9
Reflection shellResolution: 1.54→1.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 52224 / CC1/2: 0.67 / Rrim(I) all: 1.34 / % possible all: 98.2

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cd0

6cd0


Resolution: 1.54→80 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 1320 0.4 %random
Rwork0.1287 ---
obs0.1289 328680 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.54→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14937 0 333 1936 17206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONbonds0.00515806
X-RAY DIFFRACTIONangles0.78921303

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