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

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Basic information

Entry
Database: PDB / ID: 6uxh
TitleStructure of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP
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
Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.858 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6323
Polymers104,5702
Non-polymers621
Water6,882382
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,2656
Polymers209,1414
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Unit cell
Length a, b, c (Å)55.640, 126.820, 128.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 52285.203 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.175 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 19.5% (w/v) PEG MME 2000

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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: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→47.37 Å / Num. obs: 78106 / % possible obs: 99.6 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.03 / Rrim(I) all: 0.106 / Net I/σ(I): 19.2 / Num. measured all: 957925 / Scaling rejects: 630
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.124 / Num. measured all: 29349 / Num. unique obs: 4367 / CC1/2: 0.636 / Rpim(I) all: 0.888 / Rrim(I) all: 2.306 / Net I/σ(I) obs: 0.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cj0

1cj0


Resolution: 1.858→42.07 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2312 3652 4.93 %
Rwork0.1989 --
obs0.2005 74057 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 35.2396 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.858→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 4 382 7399
Biso mean--36.62 36.41 -
Num. residues----923
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.858-1.88210.3683930.3785230591
1.8821-1.90790.4862820.522149490
1.9079-1.93520.6442850.5509144652
1.9352-1.9640.39571370.3259280199
1.964-1.99470.27471610.25932776100
1.9947-2.02740.29571690.24882774100
2.0274-2.06240.35391230.31652863100
2.0624-2.09990.32031340.28672791100
2.0999-2.14030.27261540.21372801100
2.1403-2.1840.26881520.22112769100
2.184-2.23140.30481530.2686278098
2.2314-2.28340.41531500.319271598
2.2834-2.34050.25631170.22142855100
2.3405-2.40370.25551320.19822817100
2.4037-2.47450.23731650.19562810100
2.4745-2.55430.29181530.19272821100
2.5543-2.64560.23641520.19712819100
2.6456-2.75150.22051290.19492838100
2.7515-2.87670.2741560.19232813100
2.8767-3.02830.22591390.1922854100
3.0283-3.2180.20561200.1952885100
3.218-3.46630.23141560.19192871100
3.4663-3.8150.20931430.16632846100
3.815-4.36650.16661650.13612893100
4.3665-5.49940.15521760.1432901100
5.4994-42.070.16561560.16623067100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4415-0.1710.15321.96280.47321.12540.0344-0.1450.03230.15070.0044-0.0553-0.045-0.0118-0.02440.1518-0.01570.0240.2331-0.03040.1825-14.3804-8.812630.3738
20.40640.075-0.06991.27380.40231.79090.06150.0237-0.0973-0.0954-0.01610.01020.1322-0.0447-0.04980.1640.0371-0.02880.1822-0.01530.2204-13.5381-30.32078.7253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 470)A-1 - 470
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 470)B0 - 470

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