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- PDB-6uxk: Structure of serine hydroxymethyltransferase 8 from Glycine max c... -

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Basic information

Entry
Database: PDB / ID: 6uxk
TitleStructure of serine hydroxymethyltransferase 8 from Glycine max cultivar Forrest complexed with PLP
ComponentsSerine hydroxymethyltransferase
KeywordsPLANT PROTEIN / TRANSFERASE / folate metabolism / methyltransferase / soybean cyst nematode infection resistance / cytoplasmic enzyme
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / chloroplast / 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
Serine hydroxymethyltransferase / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKorasick, D.A. / Tanner, J.J. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2019-67012-29653 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode.
Authors: Korasick, D.A. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9134
Polymers104,7892
Non-polymers1242
Water3,531196
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,8268
Polymers209,5774
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Unit cell
Length a, b, c (Å)56.120, 127.970, 128.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 249 or resid 251 through 470))
21(chain B and (resid 0 through 249 or resid 251...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPROPRO(chain A and (resid 0 through 249 or resid 251 through 470))AA0 - 2492 - 251
12ALAALALYSLYS(chain A and (resid 0 through 249 or resid 251 through 470))AA251 - 470253 - 472
21HISHISPROPRO(chain B and (resid 0 through 249 or resid 251...BB0 - 2492 - 251
22ALAALAGLYGLY(chain B and (resid 0 through 249 or resid 251...BB251 - 326253 - 328
23LYSLYSLYSLYS(chain B and (resid 0 through 249 or resid 251...BB327329
24HISHISLYSLYS(chain B and (resid 0 through 249 or resid 251...BB0 - 4702 - 472
25HISHISLYSLYS(chain B and (resid 0 through 249 or resid 251...BB0 - 4702 - 472
26HISHISLYSLYS(chain B and (resid 0 through 249 or resid 251...BB0 - 4702 - 472
27HISHISLYSLYS(chain B and (resid 0 through 249 or resid 251...BB0 - 4702 - 472

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 52394.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: SHMT / Production host: Escherichia coli (E. coli)
References: UniProt: K4FW35, UniProt: A0A0R0IK90*PLUS, glycine hydroxymethyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.21 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: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.7 Å / Num. obs: 54674 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Net I/σ(I): 26.4 / Num. measured all: 1094603 / Scaling rejects: 6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.828 / Num. measured all: 62685 / Num. unique obs: 4402 / CC1/2: 0.392 / Rpim(I) all: 0.76 / Rrim(I) all: 2.937 / Net I/σ(I) obs: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXH

6uxh


Resolution: 2.1→47.696 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.6
RfactorNum. reflection% reflection
Rfree0.2251 2626 4.84 %
Rwork0.1813 --
obs0.1835 54285 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.33 Å2 / Biso mean: 54.1612 Å2 / Biso min: 26.26 Å2
Refinement stepCycle: final / Resolution: 2.1→47.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 8 196 7256
Biso mean--60.24 49.18 -
Num. residues----926
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4296X-RAY DIFFRACTION3.87TORSIONAL
12B4296X-RAY DIFFRACTION3.87TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13820.33171350.2927245192
2.1382-2.17930.33431320.285263597
2.1793-2.22380.32071260.2724266899
2.2238-2.27210.31941540.26742677100
2.2721-2.3250.3161330.23042731100
2.325-2.38310.25751330.21462666100
2.3831-2.44760.23791390.19462745100
2.4476-2.51960.2381340.19962696100
2.5196-2.60090.27841470.20162696100
2.6009-2.69390.28961120.20912745100
2.6939-2.80170.26361210.20052751100
2.8017-2.92920.29021470.19772707100
2.9292-3.08360.29821250.20342740100
3.0836-3.27680.2041340.19962773100
3.2768-3.52970.27641340.20072729100
3.5297-3.88480.2021300.1622771100
3.8848-4.44650.18211590.14052747100
4.4465-5.60080.16731420.14722835100
5.6008-47.6960.19671890.16062896100
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)
10.6925-0.19150.20562.26190.50011.4910.0622-0.18830.02070.2418-0.0426-0.0354-0.0594-0.0317-0.01470.2737-0.03590.0410.3422-0.01880.2629-14.3791-8.756130.309
20.75030.2168-0.18781.4980.4672.2730.06050.0205-0.2011-0.0638-0.025-0.04750.2405-0.0265-0.0370.28590.0452-0.03830.2783-0.02070.3428-13.6833-30.34338.7225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 470)A0 - 470
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 470)B0 - 470

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