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- PDB-9dlt: STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX C... -

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Basic information

Entry
Database: PDB / ID: 9dlt
TitleSTRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / FOLATE METABOLISM / METHYLTRANSFERASE / SOYBEAN CYST NEMATODE INFECTION RESISTANCE / CYTOPLASMIC ENZYME / PLANT PROTEIN
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation
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: 1.9 Å
AuthorsBeamer, L.J. / Owuocha, L.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2152548 United States
National Institute of Food and Agriculture (NIFA, United States)021-67013-35887 United States
CitationJournal: To Be Published
Title: STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE
Authors: Beamer, L.J. / Owuocha, L.F.
History
DepositionSep 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,89215
Polymers327,8696
Non-polymers2,0239
Water25,4191411
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)659,78430
Polymers655,73712
Non-polymers4,04718
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)174.830, 174.830, 184.113
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-852-

HOH

21E-650-

HOH

31E-664-

HOH

41F-613-

HOH

51F-737-

HOH

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Components

#1: Protein
Serine hydroxymethyltransferase


Mass: 54644.789 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100815417, GLYMA_05G152100 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R4J3C9, 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.: 6 / 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.22 M TRIMETHYLAMINE N-OXIDE, 0.1 M TRIS (PH 8.5), 20% (W/V) PEG MME 2000

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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: Oct 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→48.67 Å / Num. obs: 341703 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 27.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 16864 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→48.67 Å / SU ML: 0.2349 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 12829 5.06 %
Rwork0.1991 240756 -
obs0.2007 253585 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21189 0 132 1411 22732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007822038
X-RAY DIFFRACTIONf_angle_d0.97329942
X-RAY DIFFRACTIONf_chiral_restr0.05643247
X-RAY DIFFRACTIONf_plane_restr0.00863931
X-RAY DIFFRACTIONf_dihedral_angle_d7.73543110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.42333990.37747979X-RAY DIFFRACTION99.77
1.92-1.940.39634270.3497968X-RAY DIFFRACTION99.79
1.94-1.970.34734330.32397960X-RAY DIFFRACTION99.73
1.97-1.990.31134030.30777917X-RAY DIFFRACTION99.7
1.99-2.020.31034430.29697976X-RAY DIFFRACTION99.86
2.02-2.050.31344220.27958005X-RAY DIFFRACTION99.78
2.05-2.080.31594410.27967924X-RAY DIFFRACTION99.8
2.08-2.110.29563650.25988033X-RAY DIFFRACTION99.7
2.11-2.140.29384360.24877926X-RAY DIFFRACTION99.73
2.14-2.170.29783920.24548031X-RAY DIFFRACTION99.93
2.17-2.210.27144240.23228025X-RAY DIFFRACTION99.93
2.21-2.250.28264330.22197960X-RAY DIFFRACTION99.85
2.25-2.30.26964220.21437995X-RAY DIFFRACTION99.73
2.3-2.340.24723850.20518001X-RAY DIFFRACTION99.88
2.34-2.390.24984250.19738056X-RAY DIFFRACTION99.82
2.39-2.450.24954820.1937896X-RAY DIFFRACTION99.77
2.45-2.510.23354090.18938023X-RAY DIFFRACTION99.87
2.51-2.580.24044060.19287990X-RAY DIFFRACTION99.79
2.58-2.650.23874050.20088042X-RAY DIFFRACTION99.75
2.65-2.740.24635070.20937951X-RAY DIFFRACTION99.8
2.74-2.840.2574330.20288020X-RAY DIFFRACTION99.87
2.84-2.950.23164080.19428057X-RAY DIFFRACTION99.92
2.95-3.090.22924110.19318063X-RAY DIFFRACTION99.87
3.09-3.250.23964660.19738005X-RAY DIFFRACTION99.91
3.25-3.450.24144060.20048089X-RAY DIFFRACTION99.94
3.45-3.720.20174070.17988127X-RAY DIFFRACTION99.96
3.72-4.090.17654760.15828063X-RAY DIFFRACTION99.96
4.09-4.680.17264540.14878115X-RAY DIFFRACTION100
4.68-5.90.18954410.16518197X-RAY DIFFRACTION100
5.9-48.670.19194680.17788362X-RAY DIFFRACTION99.39

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