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- PDB-9ce6: Key structural role for the conserved cis-proline of soybean seri... -

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Basic information

Entry
Database: PDB / ID: 9ce6
TitleKey structural role for the conserved cis-proline of soybean serine hydroxymethyltransferase
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / enzyme / missense mutation / ligand complex
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
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBeamer, L.J. / Samarakoon, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 2152548 United States
National Institute of Food and Agriculture (NIFA, United States)NIFA 2021-67013-35887 United States
Citation
Journal: Biochem.J. / Year: 2024
Title: Key structural role of a conserved cis-proline revealed by the P285S variant of soybean serine hydroxymethyltransferase 8.
Authors: Samarakoon, V. / Owuocha, L.F. / Hammond, J. / Mitchum, M.G. / Beamer, L.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: 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
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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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


Theoretical massNumber of molelcules
Total (without water)108,7192
Polymers108,7192
Non-polymers00
Water4,540252
1
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase

A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)217,4384
Polymers217,4384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)116.603, 129.685, 58.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Serine hydroxymethyltransferase


Mass: 54359.438 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 BL21(DE3) (bacteria)
References: UniProt: K4FZF8, glycine hydroxymethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes, pH 7.5 20% w/v PEG 3350 2% v/v tacsimate, pH 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.57 Å / Num. obs: 43034 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 54.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Net I/σ(I): 13.5
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 2.437 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3891 / CC1/2: 0.537 / Rpim(I) all: 1.354 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→41.34 Å / SU ML: 0.3223 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 30.4795
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 2166 5.04 %
Rwork0.1914 40797 -
obs0.1946 42963 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.63 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 0 252 7018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076936
X-RAY DIFFRACTIONf_angle_d0.93779430
X-RAY DIFFRACTIONf_chiral_restr0.05111041
X-RAY DIFFRACTIONf_plane_restr0.00691236
X-RAY DIFFRACTIONf_dihedral_angle_d8.2607993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.38271500.32282649X-RAY DIFFRACTION99.89
2.3-2.360.39561380.30772702X-RAY DIFFRACTION99.93
2.36-2.420.35431490.28442666X-RAY DIFFRACTION99.93
2.42-2.50.32831390.24412672X-RAY DIFFRACTION100
2.5-2.580.31491490.24342675X-RAY DIFFRACTION99.96
2.58-2.670.35011540.24212703X-RAY DIFFRACTION99.9
2.67-2.770.33391480.22562684X-RAY DIFFRACTION100
2.77-2.90.30291420.22232709X-RAY DIFFRACTION100
2.9-3.050.26391300.20972709X-RAY DIFFRACTION99.93
3.05-3.240.26591390.19882732X-RAY DIFFRACTION99.97
3.24-3.50.2761500.20232693X-RAY DIFFRACTION99.89
3.5-3.850.24241510.16672738X-RAY DIFFRACTION99.76
3.85-4.40.2351400.15962737X-RAY DIFFRACTION99.9
4.4-5.540.20311480.16852784X-RAY DIFFRACTION99.8
5.54-41.340.23141390.17762944X-RAY DIFFRACTION99.81
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)
12.195928174750.4449671784280.2204698726913.408112230680.2690583971181.16267434782-0.018804898189-0.03470303076570.5547845929110.0351124603529-0.1544884769860.294979343835-0.1353118809470.02274848522220.1501328909230.4339370083590.02626868187560.04685075650130.4747247950810.01661028966790.61494683979728.715806462526.578594598318.8415077104
22.997277877780.781518183636-0.09890286382421.253014784090.9674828693741.440598401980.0323305037491-0.0101051940167-0.5165287424670.360921624958-0.0248895938022-0.1142761994350.50074361161-0.00922132460846-0.01507867713120.6608963305540.0152950480805-0.06222512059410.5052986438520.08991249181790.72056532332335.9948035309-1.9914600972722.9849138899
32.535828788770.0296652684236-0.3447901598233.4504206359-0.2909637270741.739365397410.206663488247-0.3783566352550.2452985376520.258240652954-0.211766503939-0.2817233087860.2839240056710.122254029968-0.01059191988070.647488159307-0.053598496782-0.02088893916450.498698590719-0.004908061464070.55962522342935.701443644611.731038725328.6634749786
42.22917267250.48589835561-0.4583198649993.43909237750.2633273883252.424530897040.02031805361240.291987393534-0.178299131758-0.640794718564-0.0211014967830.5160266736810.160523468936-0.368528384189-0.01130380048870.620252398248-0.0723763554594-0.07627085631690.5979990061320.0208030471590.66552268305115.13085921314.29289157785.38555520704
52.233061728770.9048173557380.3299694998091.901539176490.01036440014541.39282849541-0.1249102729410.1058412847940.2481850239590.00807241209031-0.06111651789240.432089261369-0.00819645146596-0.142438415320.1808754252010.4829144573450.0327045241626-0.007548167223940.4748736168390.02612287672410.68801840991228.356961334226.182122881314.3504410826
62.643961463980.1416121781480.541916140333.500790688150.01949373451881.40690600173-0.06174067869270.414250790038-0.0554517124805-0.2500844917520.148889588799-0.579925443259-0.04884941486030.351600648951-0.08530007227150.430458657974-0.00590048471960.08772257367510.566050859771-0.03592696992670.56789053616854.542628169421.31280806477.85730084919
72.042660062170.7254376899931.069876167062.422798426251.106899789613.06566600233-0.0379827139371-0.2202121833310.3615903161970.2380788728450.03676168688590.0604145423286-0.2309140088340.0521931538370.05499158482380.449391903286-0.000782474894485-0.01401460230220.458747664322-0.01305687924470.66621313214949.089023340.392719222126.7512640307
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 89 )AA0 - 891 - 90
22chain 'A' and (resid 90 through 241 )AA90 - 24191 - 231
33chain 'A' and (resid 242 through 308 )AA242 - 308232 - 296
44chain 'A' and (resid 309 through 469 )AA309 - 469297 - 452
55chain 'B' and (resid 0 through 89 )BB0 - 891 - 90
66chain 'B' and (resid 90 through 292 )BB90 - 29291 - 279
77chain 'B' and (resid 293 through 465 )BB293 - 465280 - 450

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