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- PDB-7uji: Structure of the P130R single variant of serine hydroxymethyltran... -

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Basic information

Entry
Database: PDB / ID: 7uji
TitleStructure of the P130R single variant of serine hydroxymethyltransferase 8 from Glycine max cultivar Essex complexed with PLP
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Enzyme / complex
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from L-serine / tetrahydrofolate interconversion / pyridoxal phosphate binding
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
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsKorasick, D.A. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
Citation
Journal: Febs J. / Year: 2024
Title: Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance.
Authors: Korasick, D.A. / Owuocha, L.F. / Kandoth, P.K. / Tanner, J.J. / Mitchum, M.G. / Beamer, L.J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)108,7074
Polymers108,5832
Non-polymers1242
Water4,071226
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,4148
Polymers217,1664
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Unit cell
Length a, b, c (Å)55.742, 127.006, 129.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 54291.406 Da / Num. of mol.: 2 / Mutation: P130R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380, GLYMA_08G108900 / Variant: P130R / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R0IK90, 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.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 - 0.25 M trimethylamine N-oxide, 0.1 M Tris (pH 8.5), 21-23% (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: 1.000003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000003 Å / Relative weight: 1
ReflectionResolution: 2.3→47.47 Å / Num. obs: 41612 / % possible obs: 99.74 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.14 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05908 / Rrim(I) all: 0.1577 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 27361 / CC1/2: 0.469 / Rpim(I) all: 0.9639 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1uxh

1uxh


Resolution: 2.3→47.47 Å / SU ML: 0.317 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 2119 5.1 %
Rwork0.1948 39413 -
obs0.1981 41532 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7109 0 8 226 7343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787291
X-RAY DIFFRACTIONf_angle_d0.94499877
X-RAY DIFFRACTIONf_chiral_restr0.05011065
X-RAY DIFFRACTIONf_plane_restr0.00821289
X-RAY DIFFRACTIONf_dihedral_angle_d6.89571022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.32471510.27022588X-RAY DIFFRACTION99.96
2.35-2.410.371230.2592611X-RAY DIFFRACTION99.93
2.41-2.480.30521070.2552601X-RAY DIFFRACTION99.93
2.48-2.550.32761330.25452613X-RAY DIFFRACTION100
2.55-2.630.3111390.24632591X-RAY DIFFRACTION100
2.63-2.730.3581440.26962579X-RAY DIFFRACTION99.71
2.73-2.840.25641430.22722620X-RAY DIFFRACTION100
2.84-2.970.26871530.21562613X-RAY DIFFRACTION99.93
2.97-3.120.31181390.20872609X-RAY DIFFRACTION100
3.12-3.320.25891600.20982599X-RAY DIFFRACTION99.96
3.32-3.570.32861250.22122635X-RAY DIFFRACTION99.5
3.57-3.930.2551450.18142602X-RAY DIFFRACTION98.35
3.93-4.50.21421650.15632620X-RAY DIFFRACTION99.43
4.5-5.670.21631390.15412706X-RAY DIFFRACTION99.96
5.67-47.470.20291530.15812826X-RAY DIFFRACTION99.8
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)
10.5360992281590.2793378621360.3404816333812.66166450410.7498102277311.090957043420.1085662587650.05630786735830.103368269633-0.194543328132-0.08001961442170.1289969153-0.2445167893-0.0341735432118-0.02407601050520.3171230676260.04965631050990.02331826312390.3456025604530.06072049542740.30266573253640.051424041428.141397157937.2880581881
20.626523257066-0.0796963268102-0.1331510222742.37920561491-0.003198139370991.461796956470.01582723329330.112348542535-0.06371243163070.168348262502-0.07496340582940.1205925939490.283009754102-0.112553816060.04639098389410.305779157473-0.04120837804630.003296375721270.324985117859-0.02738959173490.31628288322933.99665522471.6390463845343.3210289912
30.923100799036-0.423333616372-0.6138471391192.973621932051.236610284051.73128434123-0.03694800226440.1041645813810.111699531594-0.4955810268630.257616134782-0.581457462314-0.07154517195170.124619739088-0.1562465549720.403001947843-0.004378125877680.08058300067810.43930645207-0.04735512489080.40305543808950.93917979336.8724754070421.8683330608
40.8230602812360.429055926505-0.1520172479191.250322944850.606321256312.279744619270.1297674067670.07313267329260.0238119904668-0.2385529290970.0130087048215-0.0271574287981-0.1219932626050.0673733586555-0.1203304835820.285626674817-0.004823143036490.02677639398340.2680383491120.05768312068830.3087278036543.396753407627.419054188736.6492816424
51.11440524436-0.03116782836440.2331434566321.895194432560.5314337162882.436018018750.0635617676026-0.07075501952470.0864580876860.3347417119680.0402549597997-0.1273538893840.05451418670630.0648292173707-0.08585424612970.3315205995660.00507678647638-0.02857088888060.295893721658-0.009017831326150.29982511820648.219025639122.175253136365.8596277827
60.747794267816-0.256713599751-0.52901212641.006177060290.6993322699912.088661544520.0478715599228-0.04881171837530.1668086697980.07187514754190.105897658924-0.296928464354-0.0727780760840.246835547951-0.1284227640610.270318183682-0.0261999481017-0.03027300239470.332736413965-0.007224534057390.35587905978551.50401277328.384945149453.6000389583
71.32642804254-0.651069625289-0.4938574460451.508763239721.18947716182.214894650660.05018136361840.01971376682930.107554807396-0.0330918915425-0.1884316505880.279714331931-0.376327628544-0.7010939900260.1287725562030.3703848084730.08214391976920.02471039868090.44479029789-0.04882726323250.4437259240428.094315194342.955982592559.4498188301
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 89 )AA-1 - 891 - 91
22chain 'A' and (resid 90 through 292 )AA90 - 29292 - 289
33chain 'A' and (resid 293 through 469 )AA293 - 469290 - 462
44chain 'B' and (resid 0 through 89 )BC0 - 891 - 90
55chain 'B' and (resid 90 through 241 )BC90 - 24191 - 242
66chain 'B' and (resid 242 through 332 )BC242 - 332243 - 328
77chain 'B' and (resid 333 through 469 )BC333 - 469329 - 461

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