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- PDB-6ccz: Crystal structure of Medicago truncatula serine hydroxymethyltran... -

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Basic information

Entry
Database: PDB / ID: 6ccz
TitleCrystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3) soaked with selenourea
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer / SAD phasing
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / selenourea / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsRuszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z.
CitationJournal: Front Plant Sci / Year: 2018
Title: Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Dauter, Z.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)102,01226
Polymers99,4052
Non-polymers2,60624
Water5,855325
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,02352
Polymers198,8104
Non-polymers5,21348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)64.675, 199.686, 152.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-601-

SEY

21B-837-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase


Mass: 49816.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G7ILW0, glycine hydroxymethyltransferase
#2: Protein Serine hydroxymethyltransferase


Mass: 49588.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11445860, MTR_2g018290 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G7ILW0, glycine hydroxymethyltransferase

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Non-polymers , 4 types, 349 molecules

#3: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH4N2Se
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 55% Tacsimate pH 7.0; for SAD phasing crystals were transferred into a drop of 100% Tacsimate pH 7.0 with a single crystal of selenourea and soaked for 15 min

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9778 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.14→100 Å / Num. obs: 52956 / % possible obs: 96.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.085 / Net I/σ(I): 19.7
Reflection shellResolution: 2.14→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 7076 / Rrim(I) all: 0.88 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→83.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.882 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1007 1.9 %RANDOM
Rwork0.165 ---
obs0.166 51949 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å20 Å2
2---1.23 Å2-0 Å2
3---1.69 Å2
Refinement stepCycle: 1 / Resolution: 2.14→83.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 94 325 7226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197018
X-RAY DIFFRACTIONr_bond_other_d0.0020.026767
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9469469
X-RAY DIFFRACTIONr_angle_other_deg1.0072.99915505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31423.836305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.213151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7241544
X-RAY DIFFRACTIONr_chiral_restr0.090.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217985
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021647
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4532.4223537
X-RAY DIFFRACTIONr_mcbond_other1.4532.4223538
X-RAY DIFFRACTIONr_mcangle_it2.4553.6114407
X-RAY DIFFRACTIONr_mcangle_other2.4553.6124408
X-RAY DIFFRACTIONr_scbond_it1.8262.7923481
X-RAY DIFFRACTIONr_scbond_other1.8242.7913478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0344.0565063
X-RAY DIFFRACTIONr_long_range_B_refined5.63819.767767
X-RAY DIFFRACTIONr_long_range_B_other5.63819.7647768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.144→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 47 -
Rwork0.288 2403 -
obs--61.71 %
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)
10.1086-0.04860.04130.4425-0.00620.33160.03430.0266-0.0030.0941-0.04030.0735-0.0183-0.00650.00610.2388-0.01640.02470.0111-0.00660.0128-5.2946.48753.025
20.2541-0.2145-0.17610.77720.01490.1546-0.00660.0007-0.03130.1268-0.01430.037-0.00440.00530.02080.25570.0013-0.0040.00410.00080.0047-7.107101.20352.174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 533
2X-RAY DIFFRACTION2B82 - 533

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