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- PDB-8tqf: Crystal structure of Soybean SHMT8 in complex with PLP-glycine an... -

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Basic information

Entry
Database: PDB / ID: 8tqf
TitleCrystal structure of Soybean SHMT8 in complex with PLP-glycine and diglutamylated 5-formyltetrahydrofolate
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / complex / enzyme / soybean
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-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
Chem-PLG / : / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 Å
AuthorsOwuocha, L.F. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
CitationJournal: Front Plant Sci / Year: 2024
Title: Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean.
Authors: Owuocha, L.F. / Mitchum, M.G. / Beamer, L.J.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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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
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,00725
Polymers216,5654
Non-polymers4,44221
Water26,6261478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.208, 89.020, 146.190
Angle α, β, γ (deg.)90.000, 90.536, 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

#1: Protein
Serine hydroxymethyltransferase


Mass: 54141.355 Da / Num. of mol.: 4
Fragment: residues 71-541 (based on Uniprot numbering in A0A0R0IK90)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R0IK90
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-S8R / N-[4-({[(6R)-2-amino-5-formyl-4-hydroxy-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid


Mass: 602.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H30N8O10 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Magnesium formate dihydrate, 13% PEG 3350 0.2 M Lithium sulfate, 0.1 M Hepes pH 7.5, 25% w/v PEG 3350

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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: May 28, 2023 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→47.41 Å / Num. obs: 238872 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.062 / Rrim(I) all: 0.091 / Χ2: 0.88 / Net I/σ(I): 8.6
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 10106 / CC1/2: 0.314 / Rpim(I) all: 0.975 / Rrim(I) all: 0.091 / Χ2: 0.49 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.69→47.09 Å / SU ML: 0.2151 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.9366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2139 11964 5.01 %
Rwork0.1841 226747 -
obs0.1856 238711 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.4 Å2
Refinement stepCycle: LAST / Resolution: 1.69→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14412 0 304 1478 16194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007215413
X-RAY DIFFRACTIONf_angle_d0.995620943
X-RAY DIFFRACTIONf_chiral_restr0.05332239
X-RAY DIFFRACTIONf_plane_restr0.00842746
X-RAY DIFFRACTIONf_dihedral_angle_d9.92762296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.710.33693200.30896326X-RAY DIFFRACTION81.52
1.71-1.730.31523520.29356757X-RAY DIFFRACTION86.88
1.73-1.750.31183820.27837213X-RAY DIFFRACTION92.83
1.75-1.770.3143970.27517608X-RAY DIFFRACTION97.85
1.77-1.80.28873870.26267799X-RAY DIFFRACTION99.3
1.8-1.820.29544550.24927673X-RAY DIFFRACTION99.45
1.82-1.850.28744030.24397760X-RAY DIFFRACTION99.52
1.85-1.870.26384580.23267728X-RAY DIFFRACTION99.5
1.87-1.90.27834010.22917754X-RAY DIFFRACTION99.6
1.9-1.930.25573850.21667751X-RAY DIFFRACTION99.57
1.93-1.970.25324120.2157799X-RAY DIFFRACTION99.71
1.97-20.27113630.22257811X-RAY DIFFRACTION99.68
2-2.040.24493910.217746X-RAY DIFFRACTION99.77
2.04-2.080.24464290.20027759X-RAY DIFFRACTION99.56
2.08-2.130.23944890.19317674X-RAY DIFFRACTION99.68
2.13-2.180.22624760.19267737X-RAY DIFFRACTION99.82
2.18-2.230.21744140.18887741X-RAY DIFFRACTION99.74
2.23-2.290.2193950.18887801X-RAY DIFFRACTION99.25
2.29-2.360.21424630.18387694X-RAY DIFFRACTION99.55
2.36-2.440.22513850.18077780X-RAY DIFFRACTION99.19
2.44-2.520.23413460.18257811X-RAY DIFFRACTION98.91
2.52-2.630.22424210.18787648X-RAY DIFFRACTION97.95
2.63-2.740.2223920.17747603X-RAY DIFFRACTION97.36
2.74-2.890.21984100.17717557X-RAY DIFFRACTION96.6
2.89-3.070.20263880.17037439X-RAY DIFFRACTION94.92
3.07-3.310.18763780.16757368X-RAY DIFFRACTION93.73
3.31-3.640.20353460.16237303X-RAY DIFFRACTION92.54
3.64-4.170.15273680.14937194X-RAY DIFFRACTION91.3
4.17-5.250.16543300.15437411X-RAY DIFFRACTION92.96
5.25-47.090.19324280.18087502X-RAY DIFFRACTION93.65
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)
10.8395714967590.175031035828-0.1090788336630.521989650111-0.04202546416011.154749994830.05131084123750.09648346478450.0891645094211-0.0831362211112-0.05261232329990.0802001101267-0.190339342776-0.188496915283-0.002305527777340.2209043229480.0833495681504-0.009165048820240.159052239370.002434075519450.14824796233718.571744675831.325839366710.6747203023
21.13376955397-0.0096153375020.145725599190.8719097389450.52315551441.553567060210.01753605601810.176436613053-0.0182418431035-0.145044275343-0.1327596250450.201714526205-0.179541047874-0.267381062080.1111626893940.2080307319940.0799774429389-0.008623453682990.2140548266410.002242084096570.17826629153113.155858898628.93757387721.61716238352
31.158646319160.5778956637641.150527004382.410028502132.074556521392.34151769103-0.02123813000510.357158555644-0.0336972402831-0.253130036221-0.004553265145730.0264088023124-0.2250800089210.1385345688990.0101632595810.3394438275320.09514623320270.01720252285170.370443241029-0.03765162380660.1643600834523.215566624418.989237498-16.7351658111
40.8632533918420.1270086953510.03338926899560.586062314376-0.116338482570.9480897823590.032395872-0.0446887578797-0.0726511333775-0.0119187763724-0.0428690971894-0.0489956150642-0.1124551523740.04951795559490.006186840678880.1567441793350.0183847912560.01637312292790.1232876375490.01502139727330.13825592725137.067809542723.390571178418.1986426519
52.11166142916-0.197344506550.4400697310191.385877463660.8555409714641.434983906870.131683915867-0.154096960027-0.4734066455230.122846088499-0.0576941947277-0.01425930186020.2440127428640.0253498875346-0.01890031356740.19000211530.0235726945829-0.01092710674390.1500666778170.04145035733210.20116375903736.807393892610.901325467817.786351356
61.580323705170.9130629595050.4559868657491.307949709840.0828726368380.6625870898740.0652342223533-0.1003998062760.2874664763520.123948487792-0.1347004744260.0569755068336-0.2342021303190.09794418394390.0717206968170.250031024373-0.02417593607680.04576496035950.1900259989910.006015234033660.18841791213249.968721501339.340145498221.415389085
70.861734699944-0.0781351321044-0.2406554115520.445620085016-0.07017898303750.937851660692-0.02776942136370.1091247144-0.181177635559-0.00255062222767-0.03740326303940.08060039468250.0734384880021-0.1300336244660.05634309261930.138424833285-0.02954518286450.01144018740670.152867076315-0.03527568865030.198615230698-2.806692217655.0985919376346.1544019174
81.69735387552-0.524113097005-0.08635840310240.6150079553310.05346137751960.537151436333-0.01254710039020.0268321035835-0.162862546373-0.0124168115778-0.04208109374420.1174415766120.0261321742705-0.1490860353330.05525446078960.151432066392-0.04223833555330.003991983779310.18402793735-0.03085637289240.172763559616-15.50760849569.7395258942348.7492284166
90.9692533366610.0746606497902-0.09021636642890.570565855161-0.2222115588980.879684835733-0.0517752209946-0.0637120162653-0.08742423535150.0646005800232-0.0545310087101-0.0547511380012-0.02581034781240.1421416126840.1058650211740.172824865313-0.02305551858450.005280488019330.1622424529390.01900209474920.131207084212.666980421812.873618975658.87205192
102.47027031801-0.7172009171380.442322160742.194925263251.028654577421.50555678352-0.03832066012720.03335459419220.396412625932-0.0493548697979-0.0555753934907-0.10537479225-0.3837213524650.2136206973040.0454992576070.210156961656-0.0732358574537-0.007928562113060.1824605640290.008635045059670.15775697619912.425910205225.449648980858.8630410057
111.05502506639-0.5695809275870.6021410069531.50279855053-0.9374381467981.088139860610.0858560080038-0.000684653520196-0.181911953381-0.14837829446-0.206511816189-0.2004117408430.276816204590.2634796374290.1145914964640.2659475499960.03417746466120.05507273973930.2701954305190.08012161159760.22747138995521.2829809235-3.2702008727368.905120489
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 230 )AA0 - 2301 - 231
22chain 'A' and (resid 231 through 426 )AA231 - 426232 - 427
33chain 'A' and (resid 427 through 471 )AA427 - 471428 - 472
44chain 'B' and (resid 0 through 230 )BF0 - 2301 - 231
55chain 'B' and (resid 231 through 283 )BF231 - 283232 - 284
66chain 'B' and (resid 284 through 471 )BF284 - 471285 - 472
77chain 'C' and (resid 0 through 230 )CL0 - 2301 - 231
88chain 'C' and (resid 231 through 471 )CL231 - 471232 - 472
99chain 'D' and (resid 0 through 230 )DT0 - 2301 - 231
1010chain 'D' and (resid 231 through 283 )DT231 - 283232 - 284
1111chain 'D' and (resid 284 through 471 )DT284 - 471285 - 472

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