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- PDB-6cd0: Crystal structure of Medicago truncatula serine hydroxymethyltran... -

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Basic information

Entry
Database: PDB / ID: 6cd0
TitleCrystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer
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 / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)199,39911
Polymers199,0384
Non-polymers3617
Water25,3831409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, asymmetric unit contains one tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20810 Å2
ΔGint-106 kcal/mol
Surface area59800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.657, 201.563, 64.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 49816.586 Da / Num. of mol.: 3
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
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1409 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 55% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2017
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→90 Å / Num. obs: 203236 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 32184 / Rrim(I) all: 1.06 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCZ

6ccz


Resolution: 1.74→83.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.824 / SU B: 5.587 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1017 0.5 %RANDOM
Rwork0.175 ---
obs0.175 202206 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0 Å2
2---1.71 Å20 Å2
3---0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.74→83.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13917 0 24 1409 15350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914501
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213922
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.94219630
X-RAY DIFFRACTIONr_angle_other_deg0.954332057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32351848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98823.785634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.002152426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6661594
X-RAY DIFFRACTIONr_chiral_restr0.0840.22167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116559
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023285
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_it0.871.7467365
X-RAY DIFFRACTIONr_mcbond_other0.8681.7457363
X-RAY DIFFRACTIONr_mcangle_it1.5292.6119214
X-RAY DIFFRACTIONr_mcangle_other1.5292.6119215
X-RAY DIFFRACTIONr_scbond_it1.0291.9117136
X-RAY DIFFRACTIONr_scbond_other1.0291.9117137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7492.80810415
X-RAY DIFFRACTIONr_long_range_B_refined6.44215.55417394
X-RAY DIFFRACTIONr_long_range_B_other6.44115.55217393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.78 Å
RfactorNum. reflection% reflection
Rfree0.348 73 -
Rwork0.305 14449 -
obs--97.2 %
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)
10.09640.16940.0271.6718-0.15380.038-0.0122-0.086-0.0307-0.2781-0.0347-0.45690.0251-0.04260.04690.13790.00410.12460.08920.00330.241252.28953.59411.642
20.229-0.13790.0571.49840.10260.0339-0.01630.0905-0.02360.2275-0.0220.46620.01920.04060.03830.12870.00860.12090.07030.01240.266322.03552.76521.273
30.18960.0307-0.18480.6353-0.1710.24490.01750.0430.03320.04320.02360.13780.0057-0.0051-0.04110.10770.0004-0.0010.10320.00560.146924.58-1.14423.95
40.1887-0.0188-0.16730.51390.21830.2730.0188-0.02880.0552-0.04310.0396-0.08910.0123-0.0058-0.05840.1163-0.00910.0080.1041-0.01130.132952.901-0.2329.389
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 533
2X-RAY DIFFRACTION2B82 - 533
3X-RAY DIFFRACTION3C82 - 533
4X-RAY DIFFRACTION4D82 - 533

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