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- PDB-6cd1: Crystal structure of Medicago truncatula serine hydroxymethyltran... -

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Basic information

Entry
Database: PDB / ID: 6cd1
TitleCrystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates
Components(Serine hydroxymethyltransferase) x 2
KeywordsTRANSFERASE / PLP / one-carbon cycle / tetrahydrofolate / chloroplast / tetramer / PLP-Serine / PLP-Glycine
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity ...glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / methyltransferase activity / pyridoxal phosphate binding / methylation / mitochondrion / zinc ion binding / cytoplasm
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
ACETATE ION / GLYCINE / Chem-PLG / Chem-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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

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
G: Serine hydroxymethyltransferase
H: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,50125
Polymers397,3928
Non-polymers2,10917
Water36,6062032
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
C: Serine hydroxymethyltransferase
D: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,69913
Polymers198,3544
Non-polymers1,3459
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20190 Å2
ΔGint-92 kcal/mol
Surface area59610 Å2
MethodPISA
2
E: Serine hydroxymethyltransferase
F: Serine hydroxymethyltransferase
G: Serine hydroxymethyltransferase
H: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,80212
Polymers199,0384
Non-polymers7648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-84 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.086, 103.653, 180.379
Angle α, β, γ (deg.)90.00, 97.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABCDFEGH

#1: Protein
Serine hydroxymethyltransferase


Mass: 49588.469 Da / Num. of mol.: 5
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: 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

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Non-polymers , 6 types, 2049 molecules

#3: 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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2032 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 75 mM MES pH 6.5, 19% PEG3350 and 150 mM ammonium acetate. The mature crystals were soaked with 200 mM Ser for 2 h and cryoprotected by the addition of ethylene glycol to a final concentration of 20%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 263165 / % possible obs: 98.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Net I/σ(I): 13.3
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 41826 / Rrim(I) all: 0.83 / % possible all: 97.3

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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: 1.91→46.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.953 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1316 0.5 %RANDOM
Rwork0.191 ---
obs0.191 261832 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å20.43 Å2
2--1.24 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.91→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27693 0 138 2032 29863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01928501
X-RAY DIFFRACTIONr_bond_other_d0.0020.0227474
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.94438555
X-RAY DIFFRACTIONr_angle_other_deg0.98363228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43253615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36923.8061235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.302154784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.19515184
X-RAY DIFFRACTIONr_chiral_restr0.0870.24274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02132405
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026411
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_it1.1632.69214484
X-RAY DIFFRACTIONr_mcbond_other1.1632.69214480
X-RAY DIFFRACTIONr_mcangle_it1.8864.02918089
X-RAY DIFFRACTIONr_mcangle_other1.8864.02818088
X-RAY DIFFRACTIONr_scbond_it1.3222.90214017
X-RAY DIFFRACTIONr_scbond_other1.3222.90214017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2274.27620467
X-RAY DIFFRACTIONr_long_range_B_refined5.18522.41333302
X-RAY DIFFRACTIONr_long_range_B_other5.18522.41433303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.957 Å
RfactorNum. reflection% reflection
Rfree0.366 94 -
Rwork0.349 18654 -
obs--95.47 %
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)
10.5529-0.17890.08730.21890.09340.1929-0.02390.0504-0.02130.02520.04130.0037-0.0481-0.0342-0.01740.12420.00570.04490.1491-0.03260.08570.397934.431682.1563
20.70580.0224-0.10220.633-0.10560.1167-0.0615-0.0387-0.09510.14440.0637-0.1747-0.08210.0079-0.00220.10520.002-0.01860.1391-0.02960.115222.564416.82896.5781
30.4703-0.0150.03850.2110.08020.11850.01330.0527-0.08240.0489-0.0417-0.02660.03430.01910.02840.06590.01440.01040.2366-0.02090.059553.919120.959251.4359
40.5815-0.3315-0.10360.32570.19120.43380.12860.1633-0.0193-0.0053-0.16990.0495-0.0732-0.04960.04130.11510.0150.0140.2984-0.03310.011629.073235.030136.4603
50.28340.0675-0.06840.3496-0.03570.0414-0.0203-0.0033-0.04090.00540.0244-0.0251-0.03620.0036-0.00410.10210.02370.06610.22130.02480.062235.018986.27327.6298
60.3121-0.0206-0.20290.62130.20250.2686-0.03260.0874-0.0973-0.0746-0.02080.0774-0.0732-0.11810.05350.07850.02520.03060.2831-0.01490.051912.342869.2636-7.8058
70.5708-0.12310.11930.26850.04680.21590.0074-0.0319-0.0706-0.02430.00080.00150.0702-0.0619-0.00820.08760.02190.02680.20140.04170.059-18.601569.776536.7583
80.4562-0.24890.11740.5578-0.04090.1909-0.0603-0.07270.14040.06020.1022-0.1793-0.0131-0.0854-0.04180.09660.0759-0.0250.2071-0.03020.1036.0982.763853.1333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 533
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B83 - 533
4X-RAY DIFFRACTION2B601
5X-RAY DIFFRACTION3C82 - 533
6X-RAY DIFFRACTION3C601 - 602
7X-RAY DIFFRACTION4D83 - 533
8X-RAY DIFFRACTION4D601
9X-RAY DIFFRACTION5E83 - 533
10X-RAY DIFFRACTION5E601
11X-RAY DIFFRACTION6F83 - 533
12X-RAY DIFFRACTION6F601
13X-RAY DIFFRACTION7G83 - 533
14X-RAY DIFFRACTION7H601
15X-RAY DIFFRACTION8H82 - 533
16X-RAY DIFFRACTION8H602

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