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- PDB-7ujh: Structure of the P130R single variant of serine hydroxymethyltran... -

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Basic information

Entry
Database: PDB / ID: 7ujh
TitleStructure of the P130R single variant of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP and glycine
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
Chem-PLG / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.24 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
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 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 1.2Jan 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)104,9095
Polymers104,2342
Non-polymers6743
Water99155
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,81810
Polymers208,4694
Non-polymers1,3496
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Unit cell
Length a, b, c (Å)55.851, 126.036, 129.606
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: 52117.160 Da / Num. of mol.: 2 / Mutation: P130R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380, GLYMA_08G108900 / Variant: P130R / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0R0IK90, 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.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 - 0.25 M trimethylamine N-oxide, 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: 14-ID-B / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.24→126.04 Å / Num. obs: 44709 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 56.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.1
Reflection shellResolution: 2.24→2.31 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.42 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4053 / CC1/2: 0.996 / Rpim(I) all: 0.954 / Rrim(I) all: 2.603 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1uxi

1uxi


Resolution: 2.24→63.02 Å / SU ML: 0.3665 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 30.2904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 2285 5.11 %
Rwork0.2037 42424 -
obs0.206 44709 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.76 Å2
Refinement stepCycle: LAST / Resolution: 2.24→63.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 44 55 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727202
X-RAY DIFFRACTIONf_angle_d0.94619771
X-RAY DIFFRACTIONf_chiral_restr0.05091065
X-RAY DIFFRACTIONf_plane_restr0.00741274
X-RAY DIFFRACTIONf_dihedral_angle_d7.96891008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.290.40831340.44272520X-RAY DIFFRACTION97.5
2.29-2.340.40431400.38192619X-RAY DIFFRACTION99.46
2.34-2.40.38491460.3462593X-RAY DIFFRACTION99.89
2.4-2.470.36341560.32512619X-RAY DIFFRACTION99.89
2.47-2.540.37441450.30282623X-RAY DIFFRACTION100
2.54-2.620.30171170.28162652X-RAY DIFFRACTION99.86
2.62-2.710.3071420.27242631X-RAY DIFFRACTION99.93
2.71-2.820.31881720.2572616X-RAY DIFFRACTION99.96
2.82-2.950.26311730.24542615X-RAY DIFFRACTION99.96
2.95-3.110.30021330.23062639X-RAY DIFFRACTION99.78
3.11-3.30.27191280.21812666X-RAY DIFFRACTION99.79
3.3-3.560.27921330.222653X-RAY DIFFRACTION99.75
3.56-3.910.25721450.18152684X-RAY DIFFRACTION99.79
3.91-4.480.22061350.16192690X-RAY DIFFRACTION99.93
4.48-5.640.21461370.16232743X-RAY DIFFRACTION99.97
5.64-63.020.16291490.15872861X-RAY DIFFRACTION99.54
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)
10.4272309823710.0382973245718-0.2135792537722.649224242760.2518678578411.439778559720.1847281948230.0208025287266-0.1374117813020.0593678401323-0.1039934249470.2644556272830.347563690299-0.0612534354854-0.1009411726260.655351093842-0.061271927033-0.04823239429230.58944400650.03384385303220.54793248147-15.9292878114-28.277044942527.1575594004
20.382746388481-0.1285356038960.319024149882.13433263539-0.3474662554741.912416981560.0918899012111-0.05868655556920.136440111745-0.201831396831-0.1216808237950.0473130152179-0.200214646399-0.09351668975480.01124352269250.517411027014-0.00198141310889-0.005308768276610.58240430443-0.03012804758290.553940592505-17.3991506827-3.0316248531417.2989934414
30.546791079202-0.9505196311140.6220106576010.781844705998-0.142960956412.24261172856-0.154680362562-0.1589947506480.335738208690.268505380316-0.004771952618460.129946213876-0.713893468071-0.05394128162120.06593722247250.738576135648-0.0110245809230.004547514278660.610710235149-0.08934423790220.58456132013-18.17526728179.8936979991525.2254688508
41.175053493050.2397251826840.1330698647732.840556049010.4655296008961.651213391240.0454166825695-0.0997667509090.02717373805730.0943288859762-0.03284452953770.375104099189-0.00785114695492-0.301845699303-0.04882672688230.5304636374190.007549014651220.04056316423520.615388023827-0.01976764940980.562391387934-25.1473616075-6.9877504827127.6201947741
51.959558368140.4233222517530.6003768137562.757560937410.5543882928411.821946322460.1417104217830.0324475220058-0.1659832519720.1592326511850.0551930928529-0.454198733302-0.09054368800890.0381176144188-0.143888543330.709047377645-0.0526018276477-0.05055825163450.692653687435-0.09081811785720.705800854841-2.919115566461.5428804081840.1813970301
62.248920759751.247755570890.7277812034542.425806617170.5908967799831.60637299413-0.0524707054925-0.00280718556330.08178109889260.6081579094450.355483145526-0.6749689738640.1492487420790.230040258147-0.194305779840.715256738016-0.0153845290135-0.09888844249390.695716929979-0.09610187313080.693548852256-2.47708819032-3.9508468404643.8276115213
7-0.3308280399341.371894337320.7445640749620.6455533777271.113879229230.9391226511190.2641508908110.0440112627204-0.395724729080.8163640363320.278279687294-0.887699878380.3561613587730.325442300888-0.3001055545930.9922992053490.0283386354012-0.213476436090.797907619202-0.06012726994311.002958154612.86192923247-15.538900814845.3596860311
81.02442170801-0.06337163724690.1449669691031.747734904880.238765440512.036131509180.118974038743-0.228075586067-0.01819129426410.240446593498-0.1126958949640.01857844744270.136638657970.1370545746050.04419165781530.625544234665-0.000806728274353-0.02181768827950.5381474637450.04485825173330.527688562436-12.3169288958-27.612200725227.7641194325
90.5381728004870.323154802622-0.6721962871841.25974152605-0.5013510017682.620313363960.1140244833280.0930230062531-0.0933151586399-0.384494492425-0.0089246645374-0.023106269152-0.15781490721-0.164401719712-0.04174869519950.5519044913670.0138044614753-0.02832993457730.5219239556250.01228521000730.565874784768-10.3517856282-17.01443593382.97802861363
101.376084265370.03354550802070.04289234801221.980127752610.03112209504740.9421715958920.02498020562730.136880345085-0.112641142209-0.49154519696-0.000351841084256-0.06698559252770.06599823032620.257418910284-0.01268344035070.7612101125810.0421216041565-0.007535726371020.556426434353-0.04367946960740.574257980543-4.95779454369-26.1346216739-4.71674668177
110.915272680795-0.3151919463890.892981971210.3119377274470.008168528941731.89405950296-0.07452263591240.5584979440250.0101819516978-0.3281968282340.210839469791-0.257429077799-0.2444644695790.296167663401-0.0535505943570.686306856123-0.05202418023530.09586567045540.66346606658-0.02112641425830.5685662366961.79092199817-22.37687684518.13236673654
120.908747541856-0.1829948759430.3304548286521.257430479980.1031789689582.188994806790.121254737295-0.0670580854627-0.2573294762710.01475904797940.0116701340949-0.4962700032330.1512341044170.22505301239-0.09566082116030.4840721742520.01772520455140.0198053164190.505220704888-0.010692530220.509604540884-6.92454044543-31.6798315412.7526056577
133.100977706261.227009487611.470930139111.6541093010.3989228471491.825082440590.0137293486256-0.0882930370840.330199749488-0.405305562960.02131152179840.2615646254780.17335601135-0.3213297229170.1469133942310.726408866046-0.0616880604486-0.09465096586860.6925779578-0.0357833593430.668379701994-25.0029799151-39.7328753178-2.18699879239
142.106081182570.417400150151.122791825521.185715464150.7981911161141.712631833230.154952035023-0.084330443906-0.07532586106870.0429428156565-0.3340194724120.3150393018380.338017574637-0.6972343127740.1260898709190.762191114229-0.0762915773939-0.03439865094640.753408267188-0.1026069487020.757928551072-29.2526903935-42.55470885083.03186030701
150.5206960974430.227236136561-0.9695400443681.837698898140.2112714808551.274568841890.197445408718-0.0707810567002-0.3468841085430.512958932885-0.102786985223-0.2983882104920.232249107119-0.5875383743490.04309574951790.917365701611-0.1045752616940.01669716002960.7379218381830.104395495130.750038219725-26.3723862331-47.303336348419.9607672237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 89 )AA-1 - 891 - 91
22chain 'A' and (resid 90 through 159 )AA90 - 15992 - 161
33chain 'A' and (resid 160 through 197 )AA160 - 197162 - 199
44chain 'A' and (resid 198 through 332 )AA198 - 332200 - 330
55chain 'A' and (resid 333 through 367 )AA333 - 367331 - 365
66chain 'A' and (resid 368 through 426 )AA368 - 426366 - 419
77chain 'A' and (resid 427 through 470 )AA427 - 470420 - 463
88chain 'B' and (resid 0 through 90 )BC0 - 901 - 91
99chain 'B' and (resid 91 through 159 )BC91 - 15992 - 160
1010chain 'B' and (resid 160 through 241 )BC160 - 241161 - 242
1111chain 'B' and (resid 242 through 275 )BC242 - 275243 - 272
1212chain 'B' and (resid 276 through 332 )BC276 - 332273 - 329
1313chain 'B' and (resid 333 through 367 )BC333 - 367330 - 364
1414chain 'B' and (resid 368 through 440 )BC368 - 440365 - 431
1515chain 'B' and (resid 441 through 469 )BC441 - 469432 - 460

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