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- PDB-8dsk: Structure of the N358Y variant of serine hydroxymethyltransferase... -

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Basic information

Entry
Database: PDB / ID: 8dsk
TitleStructure of the N358Y variant of serine hydroxymethyltransferase 8 in complex with PLP, glycine, and formyl tetrahydrofolate
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-FFO / Chem-PLG / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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)220,44530
Polymers216,2094
Non-polymers4,23626
Water37,8862103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31240 Å2
ΔGint-63 kcal/mol
Surface area57680 Å2
Unit cell
Length a, b, c (Å)87.106, 90.798, 147.441
Angle α, β, γ (deg.)90.000, 90.551, 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: 54052.281 Da / Num. of mol.: 4 / 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-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 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2103 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.18-0.25 triethylamine 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: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.63→90.8 Å / Num. obs: 281201 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.052 / Rrim(I) all: 0.102 / Net I/σ(I): 8.1
Reflection shellResolution: 1.63→1.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.336 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 12043 / CC1/2: 0.381 / Rpim(I) all: 0.801 / Rrim(I) all: 1.656 / % possible all: 84.9

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Processing

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

6uxj


Resolution: 1.63→74.68 Å / SU ML: 0.2066 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.2853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 14054 5 %
Rwork0.1845 266872 -
obs0.186 280926 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.46 Å2
Refinement stepCycle: LAST / Resolution: 1.63→74.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14474 0 288 2103 16865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007115472
X-RAY DIFFRACTIONf_angle_d0.961521005
X-RAY DIFFRACTIONf_chiral_restr0.05322239
X-RAY DIFFRACTIONf_plane_restr0.00712740
X-RAY DIFFRACTIONf_dihedral_angle_d8.63922215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.640.32443450.30067078X-RAY DIFFRACTION77.55
1.64-1.660.30674500.2918835X-RAY DIFFRACTION96.97
1.66-1.680.3394760.29448777X-RAY DIFFRACTION97.06
1.68-1.710.30565020.28228851X-RAY DIFFRACTION97.39
1.71-1.730.31194800.26968693X-RAY DIFFRACTION96.74
1.73-1.750.29364890.25868570X-RAY DIFFRACTION94.17
1.75-1.780.28354430.24858915X-RAY DIFFRACTION97.94
1.78-1.80.2814810.25028891X-RAY DIFFRACTION98.32
1.8-1.830.29434790.25468878X-RAY DIFFRACTION98.12
1.83-1.860.27964300.23488998X-RAY DIFFRACTION98.4
1.86-1.890.24014700.21759015X-RAY DIFFRACTION98.36
1.89-1.930.23494500.19878943X-RAY DIFFRACTION98.65
1.93-1.960.2394410.19739026X-RAY DIFFRACTION98.64
1.96-20.2274580.18628934X-RAY DIFFRACTION98.58
2-2.050.20984280.18019033X-RAY DIFFRACTION98.74
2.05-2.10.21514790.18098988X-RAY DIFFRACTION98.7
2.1-2.150.21674670.18268912X-RAY DIFFRACTION98.49
2.15-2.210.20634520.18559047X-RAY DIFFRACTION98.6
2.21-2.270.23585350.18848919X-RAY DIFFRACTION98.64
2.27-2.350.21114630.19138981X-RAY DIFFRACTION98.49
2.35-2.430.21874330.19268898X-RAY DIFFRACTION97.44
2.43-2.530.22715050.19238852X-RAY DIFFRACTION97.41
2.53-2.640.23354830.18599043X-RAY DIFFRACTION99.19
2.64-2.780.23244850.18919067X-RAY DIFFRACTION99.49
2.78-2.950.22174460.18619097X-RAY DIFFRACTION99.3
2.95-3.180.21994710.18239091X-RAY DIFFRACTION99.29
3.18-3.50.194750.17689150X-RAY DIFFRACTION99.43
3.5-4.010.17694730.15379106X-RAY DIFFRACTION99.35
4.01-5.050.16685150.14589039X-RAY DIFFRACTION98.38
5.05-74.680.19515500.16819245X-RAY DIFFRACTION99.35
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)
10.7370633154420.145114894426-0.205136831790.334160847887-0.1630324376560.8342989903070.01073465395130.07612141569830.0619135545205-0.0528607239894-0.02657866949020.0329429120267-0.12803454733-0.08965516853120.01054627655340.231009284750.0472236156463-0.0007475577638010.1710907092250.01186459726260.18015536111618.361306366631.114622801210.6412299841
20.9002704691280.2247070927380.2200570996920.7574058501670.8018426232092.07613459838-0.008215411974010.107212280688-0.0217350043341-0.0272666875673-0.079180552940.131593912066-0.0145362774245-0.24262697010.09028857017030.2225023855540.05181163449290.003390218221980.2098692607250.02985123925570.20609599238912.785226483928.54490661241.23346605939
30.661927391090.01918663225220.6103869664561.787185288611.343363221611.622766582270.06894289706940.180790328731-0.0978535128365-0.0126073631857-0.143669233905-0.03781862848930.1903621525530.2129746539910.07403751882380.3646534211970.09499922303530.04696068693750.369445975883-0.0004248221418660.21032898319123.086209127217.9055043918-16.7851815078
40.520027175183-0.002661861002710.1411329179220.532713881035-0.2763062833610.9138095525250.003696890136670.0327652373706-0.01061928779880.00609722685578-0.0300298880783-0.0365952437082-0.0860746083110.06518667858050.0228029018480.1779842480260.006353498199390.01855755589620.1520530556870.01354671400890.16815093552437.011658378123.42410061718.4420887048
51.401351298960.6271700699220.3399008989631.13048075701-0.1244020594491.009897032470.0071486104417-0.01855501812040.1600141301960.122882078817-0.0898994762742-0.00621050811128-0.2119062655480.1516049075850.08888007970840.214003655029-0.01046290757840.02619716193010.1710045762640.02871065356210.17116506421847.176651386132.885693399920.6942067927
60.4879248073560.0425758973721-0.1927391612120.302526834325-0.1227612382060.611623295525-0.009180225656850.0561661840321-0.0921325502693-0.0139429388095-0.01736605956420.03638881993130.0576454552996-0.0751620206480.02407122572440.182699193507-0.0145592759740.008361185947060.192584018319-0.0242032409590.224834646496-3.103827978575.3221725600646.0722707935
71.08309242066-0.321568757815-0.1299093558730.5548614826190.0413038054840.4799823490440.01258910952290.0171535608701-0.066566677711-0.0458435695079-0.01808430472140.0724165222009-0.00801925310133-0.0875517766590.00684965593970.186649594785-0.03588831807260.002237606661590.209082389804-0.01772134945330.211436154279-16.11868001510.199559675749.0613277199
80.6627055459090.185479989369-0.07207179875950.508349036471-0.1718055339490.49332895827-0.014337335479-0.0669814839272-0.05458113387630.017248250194-0.0331515392323-0.0510451350863-0.0137542614560.05088640854380.05319265608480.184374506742-0.009494455478540.006600001033050.185593703740.005209779410860.1910275501612.534121724812.582608173559.2083147441
90.997835276439-0.0852800155790.3221593405251.06527788265-0.8824897196881.293311893070.0480288893943-0.0459986272326-0.126961956057-0.148837145739-0.1788391193-0.1936981859430.2168731743480.2212685489160.115735603860.1972333970990.02087754307440.04707874484410.1828321723620.02140416702950.18168603797319.2714202143.0747944386366.9074989472
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 )BG0 - 2301 - 231
55chain 'B' and (resid 231 through 471 )BG231 - 471232 - 470
66chain 'C' and (resid 0 through 230 )CL0 - 2301 - 231
77chain 'C' and (resid 231 through 471 )CL231 - 471232 - 472
88chain 'D' and (resid 0 through 230 )DP0 - 2301 - 231
99chain 'D' and (resid 231 through 471 )DP231 - 471232 - 472

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