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- PDB-8dom: Structure of the N358Y single variant ofserine hydroxymethyltrans... -

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Basic information

Entry
Database: PDB / ID: 8dom
TitleStructure of the N358Y single variant ofserine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Enzyme / complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding
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
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKorasick, D.A. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
CitationJournal: Febs J. / Year: 2024
Title: Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.
Authors: Korasick, D.A. / Owuocha, L.F. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J.
History
DepositionJul 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,8993
Polymers108,8372
Non-polymers621
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-60 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.967, 128.599, 128.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 54418.543 Da / Num. of mol.: 2 / Mutation: N358Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380, GLYMA_08G108900 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0R0IK90, glycine hydroxymethyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.18 - 0.25 TMAO 0.1 M Tris (ph 8.5) 21-23 (w/v) % PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.89→128.63 Å / Num. obs: 75185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 44.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Net I/σ(I): 17
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 7.6 % / Rmerge(I) obs: 4.323 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 33413 / CC1/2: 0.339 / Rpim(I) all: 1.678 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6uxh

6uxh


Resolution: 1.89→64.31 Å / SU ML: 0.2962 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 25.8322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 3673 4.96 %
Rwork0.1803 70353 -
obs0.1822 74026 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.4 Å2
Refinement stepCycle: LAST / Resolution: 1.89→64.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 4 376 7547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087379
X-RAY DIFFRACTIONf_angle_d1.039910017
X-RAY DIFFRACTIONf_chiral_restr0.05591082
X-RAY DIFFRACTIONf_plane_restr0.0081311
X-RAY DIFFRACTIONf_dihedral_angle_d6.8061043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.42981090.46141933X-RAY DIFFRACTION71.95
1.91-1.940.39851160.40762528X-RAY DIFFRACTION92.16
1.94-1.970.35491370.34912622X-RAY DIFFRACTION98.71
1.97-20.40431300.31582769X-RAY DIFFRACTION99.49
2-2.030.34381770.29672653X-RAY DIFFRACTION99.79
2.03-2.060.3291380.27492719X-RAY DIFFRACTION99.86
2.06-2.10.30991370.27812699X-RAY DIFFRACTION99.86
2.1-2.140.33431620.26332711X-RAY DIFFRACTION99.9
2.14-2.180.28321260.24142715X-RAY DIFFRACTION99.96
2.18-2.220.2831470.24272746X-RAY DIFFRACTION99.93
2.22-2.270.31271280.23192720X-RAY DIFFRACTION99.96
2.27-2.320.26021350.22352717X-RAY DIFFRACTION99.93
2.32-2.380.27761550.21372720X-RAY DIFFRACTION99.72
2.38-2.450.27191330.20362715X-RAY DIFFRACTION99.93
2.45-2.520.23081610.18542711X-RAY DIFFRACTION99.93
2.52-2.60.23641520.18282735X-RAY DIFFRACTION99.93
2.6-2.690.24421600.19012719X-RAY DIFFRACTION99.9
2.69-2.80.22961370.19262782X-RAY DIFFRACTION99.73
2.8-2.930.26571450.20142741X-RAY DIFFRACTION99.93
2.93-3.080.20521320.2032729X-RAY DIFFRACTION99.79
3.08-3.270.23671390.18422774X-RAY DIFFRACTION99.9
3.27-3.530.20571300.18242773X-RAY DIFFRACTION99.97
3.53-3.880.17841600.16052770X-RAY DIFFRACTION100
3.88-4.440.171510.13452813X-RAY DIFFRACTION100
4.44-5.60.16051450.13832847X-RAY DIFFRACTION99.93
5.6-64.310.19541310.14822992X-RAY DIFFRACTION99.97
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)
10.8611481340520.2003960690570.1581514521542.434920972040.620543220021.355264081830.09829565792970.08139823559890.0987890704703-0.0831406318456-0.06981310265570.104381036326-0.253247189066-0.105861764509-0.02900188754420.3388784932180.0475864822721-0.001828850386980.3575471962290.0662395124370.311407803066-43.918463387627.610933303236.853103005
20.717206455650.08108818442290.0920091024392.36475641240.06565166374841.853731784580.06700713480050.103337327433-0.08654260238580.0198176290256-0.06998127464840.08806953421960.285632458626-0.110351582491-0.0007372541558020.384118833032-0.0168272019309-0.00846471555590.399909031185-0.02198467304140.372474548336-48.30620150260.20657266696141.617163463
30.671835556543-0.489217314147-0.5001917407592.710754877480.9868979148321.753885038340.07393022621130.158099320772-0.0203428055386-0.1371060436-0.0849593090158-0.02568059983970.170595128991-0.1845270976370.03471130244360.351122883627-0.0153410969-0.04442765511850.409810633101-0.001696611579310.351344772383-45.19138662876.1880517482931.8636259712
41.53490712283-1.51444884762-0.1473559860554.087933668131.013309468731.631627858890.1845863108360.1580989286170.232862701471-0.5846241724720.153585842451-0.914162730167-0.0308274488720.275619330903-0.3328141980990.50499514843-0.01604256281390.1158005837330.505349667343-0.07342104378340.520610798358-27.47361557967.7787018823820.5112250277
50.507728913725-0.115701704310.3249262102410.990929195589-0.02965381468781.968175774280.08055395788310.03428185867740.123781641549-0.06614889272460.00116603155229-0.1017630846510.04175349309390.0486452156275-0.08148744745250.3486005792260.004932437360110.02309942669070.3837763544790.008642075274230.430094605992-39.400851613723.053495863647.0035555666
61.49443982002-1.246436325660.2478753654694.354470366480.8072032061391.30159783503-0.0938105149754-0.3071649677570.08376327632920.6687629068450.156434717147-0.02652256204160.1036826666010.0822492376785-0.05120280014980.533441488074-0.0256443575847-0.001818652607940.453225144597-0.04479407314410.406704558998-37.795086522725.217316972174.3948169008
70.475477602882-0.00501943865255-0.2450104474821.310575466050.9415509235832.64982686060.069608692277-0.01909480100680.1531672285970.1100692584130.0281121339883-0.243400835448-0.01940582630370.303440665837-0.09266131656120.338981600247-0.035819926175-0.003431941459650.3604564378-0.007587648966290.437744026152-31.049211151627.763962397657.305419683
81.7358712652-0.427926527409-0.9946768307451.400266004261.002094041044.097564880860.0853494845450.1204883879740.13187577753-0.038521517893-0.2376793139060.243230608748-0.45983171648-0.764939570120.1291315710540.4622631081220.08648246916540.01673384397530.462640921141-0.06699634223640.47251462583-55.659544573642.818456825659.0916595605
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 90 )AA0 - 901 - 91
22chain 'A' and (resid 91 through 257 )AA91 - 25792 - 258
33chain 'A' and (resid 258 through 367 )AA258 - 367259 - 364
44chain 'A' and (resid 368 through 470 )AA368 - 470365 - 467
55chain 'B' and (resid 0 through 159 )BB0 - 1591 - 160
66chain 'B' and (resid 160 through 197 )BB160 - 197161 - 198
77chain 'B' and (resid 198 through 332 )BB198 - 332199 - 329
88chain 'B' and (resid 333 through 470 )BB333 - 470330 - 467

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