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- PDB-9kro: Crystal structure of SHMT from E. faecium with mangiferin -

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Basic information

Entry
Database: PDB / ID: 9kro
TitleCrystal structure of SHMT from E. faecium with mangiferin
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / mangiferin / xanthone glycoside / 1C-methabolism / folate
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / cytosol
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
Mangiferin / Chem-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMurayama, K. / Hayashi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K07918 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Binding of a potential antibacterial drug, mangiferin, to serine hydroxymethyltransferase from Enterococcus faecium.
Authors: Hayashi, H. / Hasegawa, K. / Saijo, E. / Kodama, E.N. / Murayama, K.
History
DepositionNov 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)91,5276
Polymers90,0102
Non-polymers1,5174
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-42 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.820, 118.820, 163.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45005.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_ ...Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_600996, EB12_01905, EfmAA708_21800, F6440_11360, GBM44_11330, GBM73_12625, GJ652_13105, SAMEA3893517_00378
Production host: Escherichia coli (E. coli)
References: UniProt: A0A133CK16, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HZI / Mangiferin / 2-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1,3,6,7-tetrakis(oxidanyl)xanthen-9-one


Mass: 422.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01M magnesium chloride, 0.05M MES (pH5.8), 1.9M lithium sulfate, 2mM mangiferin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.1 Å / Num. obs: 56242 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 48.71 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 5508 / CC1/2: 0.542

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.07 Å / SU ML: 0.2603 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9557 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2151 2000 3.56 %
Rwork0.1755 54163 -
obs0.1769 56163 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.86 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 104 199 6554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766483
X-RAY DIFFRACTIONf_angle_d0.96938808
X-RAY DIFFRACTIONf_chiral_restr0.05131002
X-RAY DIFFRACTIONf_plane_restr0.00511137
X-RAY DIFFRACTIONf_dihedral_angle_d3.70333836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.31711400.27033804X-RAY DIFFRACTION100
2.31-2.370.29371410.24913814X-RAY DIFFRACTION100
2.37-2.440.29981410.23953817X-RAY DIFFRACTION100
2.44-2.520.26021400.22333788X-RAY DIFFRACTION99.97
2.52-2.610.30241410.21483821X-RAY DIFFRACTION100
2.61-2.710.22591420.19973832X-RAY DIFFRACTION100
2.71-2.830.24221410.18873837X-RAY DIFFRACTION100
2.83-2.980.21941420.18153829X-RAY DIFFRACTION100
2.98-3.170.24741420.1853852X-RAY DIFFRACTION100
3.17-3.420.22971420.18223866X-RAY DIFFRACTION100
3.42-3.760.21641440.17043882X-RAY DIFFRACTION99.98
3.76-4.30.18671450.15123918X-RAY DIFFRACTION100
4.3-5.420.19191450.15483950X-RAY DIFFRACTION100
5.42-48.070.18251540.16054153X-RAY DIFFRACTION99.95

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