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- PDB-6uxj: Structure of serine hydroxymethyltransferase 8 from Glycine max c... -

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Basic information

Entry
Database: PDB / ID: 6uxj
TitleStructure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP-glycine and 5-formyltetrahydrofolate
ComponentsSerine hydroxymethyltransferase
KeywordsPLANT PROTEIN / TRANSFERASE / folate metabolism / methyltransferase / soybean cyst nematode infection resistance / cytoplasmic enzyme
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / chloroplast / methyltransferase activity / pyridoxal phosphate binding / methylation
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
Chem-FFO / Chem-PLG / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKorasick, D.A. / Tanner, J.J. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2019-67012-29653 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode.
Authors: Korasick, D.A. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,40229
Polymers208,2284
Non-polymers4,17425
Water30,8421712
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31230 Å2
ΔGint-65 kcal/mol
Surface area57710 Å2
Unit cell
Length a, b, c (Å)86.889, 90.764, 146.850
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine hydroxymethyltransferase


Mass: 52057.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: SHMT / Production host: Escherichia coli (E. coli)
References: UniProt: K4FZF8, UniProt: A0A0R0IK90*PLUS, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical
ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N7O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1712 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.24 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 20% (w/v) PEG MME 2000, 10 mM 5-formyl tetrahydrofolate, 20 mM glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→47.95 Å / Num. obs: 440251 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Rrim(I) all: 0.083 / Net I/σ(I): 10.2 / Num. measured all: 1533812 / Scaling rejects: 1836
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.019 / Num. measured all: 68936 / Num. unique obs: 21837 / CC1/2: 0.504 / Rpim(I) all: 0.67 / Rrim(I) all: 1.225 / Net I/σ(I) obs: 1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXH

6uxh


Resolution: 1.4→45.382 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 18.59
RfactorNum. reflection% reflection
Rfree0.1937 21586 4.92 %
Rwork0.1645 --
obs0.1659 438826 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.95 Å2 / Biso mean: 19.205 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.4→45.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14533 0 420 1713 16666
Biso mean--18.05 27.39 -
Num. residues----1887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.31246940.27441365697
1.4159-1.43260.30047550.26561389799
1.4326-1.450.28568080.26461404899
1.45-1.46840.30547790.25571395999
1.4684-1.48770.28437410.25211399999
1.4877-1.50810.27927320.232813976100
1.5081-1.52960.30287180.26451382997
1.5296-1.55250.25797020.20791405599
1.5525-1.57670.22017810.175513994100
1.5767-1.60260.21637410.166114104100
1.6026-1.63020.20546960.155714143100
1.6302-1.65990.19816700.151614125100
1.6599-1.69180.19167740.147614068100
1.6918-1.72630.19477120.150514125100
1.7263-1.76390.1886900.146814128100
1.7639-1.80490.19316800.147414149100
1.8049-1.850.196840.160514284100
1.85-1.90010.237220.18391389599
1.9001-1.9560.24487130.20171334595
1.956-2.01910.19746990.154814211100
2.0191-2.09130.21876600.18731328494
2.0913-2.1750.18746640.15441413099
2.175-2.2740.20646990.1811320393
2.274-2.39390.17987180.15421402399
2.3939-2.54380.17737810.14891385298
2.5438-2.74020.18017090.15051375597
2.7402-3.01590.17787390.14961385798
3.0159-3.45220.17526730.15681358995
3.4522-4.34890.15647380.13971349194
4.3489-45.3820.14927140.1421406697

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