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- PDB-7q00: Crystal structure of serine hydroxymethyltransferase, isoform 4 f... -

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Basic information

Entry
Database: PDB / ID: 7q00
TitleCrystal structure of serine hydroxymethyltransferase, isoform 4 from Arabidopsis thaliana (SHM4)
ComponentsSerine hydroxymethyltransferase 4
KeywordsTRANSFERASE / C1 metabolism / tetrahydrofolate / tetramer / PLP-dependent enzyme / cytosol
Function / homology
Function and homology information


salicylic acid binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / plasmodesma / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process ...salicylic acid binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / plasmodesma / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / circadian rhythm / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / plasma membrane / cytoplasm / cytosol
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 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRuszkowski, M. / Sekula, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Plant Physiol Biochem. / Year: 2022
Title: Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives.
Authors: Nogues, I. / Sekula, B. / Angelaccio, S. / Grzechowiak, M. / Tramonti, A. / Contestabile, R. / Ruszkowski, M.
History
DepositionOct 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase 4
B: Serine hydroxymethyltransferase 4
C: Serine hydroxymethyltransferase 4
D: Serine hydroxymethyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,61511
Polymers209,1214
Non-polymers4957
Water33,7421873
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23630 Å2
ΔGint-104 kcal/mol
Surface area62430 Å2
Unit cell
Length a, b, c (Å)59.091, 130.914, 121.778
Angle α, β, γ (deg.)90.000, 92.261, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Serine hydroxymethyltransferase 4 / AtSHMT4 / Glycine hydroxymethyltransferase 4 / Serine methylase 4


Mass: 52280.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM4, SHMT4, At4g13930, dl3005c, FCAALL.160 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O23254, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1873 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: D9 Index (Hampton Research); 0.1 M Tris 8.5, 25% w/v, Polyethylene glycol 3,350 cryoprotection with the reservoir condition supplemented with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2018
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→80 Å / Num. obs: 181530 / % possible obs: 95.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 23.65 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.62
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 29467 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6smr

6smr


Resolution: 1.74→49.89 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.2338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 1088 0.6 %
Rwork0.1615 180406 -
obs0.1618 181494 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.74→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14647 0 32 1873 16552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007815059
X-RAY DIFFRACTIONf_angle_d0.979820389
X-RAY DIFFRACTIONf_chiral_restr0.05442189
X-RAY DIFFRACTIONf_plane_restr0.00782659
X-RAY DIFFRACTIONf_dihedral_angle_d13.82775531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.820.30491360.255422534X-RAY DIFFRACTION95.93
1.82-1.910.24981370.218722648X-RAY DIFFRACTION95.99
1.91-2.030.22761360.191222554X-RAY DIFFRACTION95.69
2.03-2.190.22031380.161822803X-RAY DIFFRACTION96.75
2.19-2.410.20831360.162222623X-RAY DIFFRACTION96.03
2.41-2.760.22981350.165822279X-RAY DIFFRACTION94.35
2.76-3.470.19751370.157622658X-RAY DIFFRACTION95.66
3.47-49.890.1591330.137522307X-RAY DIFFRACTION93.57
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)
10.2716819093850.0722987013390.05826965664130.9680167055140.06044713427680.6266639536650.0130988505736-0.00706181920440.03843031587170.066109796419-0.0205284547041-5.88488632459E-5-0.0520282097870.01028748202720.008117058324240.1862886659450.0076768162055-0.009895843476630.1366045454820.0001597238424460.119735800252-20.5889758378-8.95888450272-5.40030176476
21.203071026870.175508771314-0.1174401697231.367278709710.1701326033571.54687856057-0.02604171286740.05638097980030.180276595676-0.0814254206455-0.0269566205810.117504585239-0.0867000724486-0.1259990341550.03094981620880.1854539805940.00733336340615-0.01169078231860.1202717122870.0005843840566170.148366857641-29.5258145703-11.0845820694-8.6457369966
31.271103352550.4586687905070.08674086785491.721966293580.4053577528170.9543850305010.0842155165087-0.09993685892720.02633823613110.3192382052580.0221582542752-0.342124281657-0.02245903776280.175318844964-0.07702878192370.296505666911-0.00657336582851-0.07397711313490.213847970734-0.02570106667020.186629463321-5.07049741929-4.2867713290114.2172802865
40.3652242380270.0443056862173-0.03287004040240.5672088093290.08839092353570.492000253563-0.01201537075150.048596900904-0.00827800408550.008564891344380.0427766817076-0.07151524825970.01128825173750.0514945562322-0.03212814070520.1801454230460.000877400118394-0.01691230656750.160118068764-0.005229407076490.152762565742-11.3364226771-23.8484894446-19.1733294958
51.557246284190.02995096196350.2476254779911.766237297770.3117676518471.12712693672-0.01126990934150.1558802062760.00985631693506-0.07262739107290.0443025382733-0.300857280171-0.1048413285070.172234890287-0.07140694523950.1927042996380.003653117590750.001403759582590.189991983688-0.01158969753770.169311692145-2.32169334768-20.925235391-16.4922966443
61.260689097020.1407823137930.1498070187950.9110578985260.3644526200991.09776218111-0.009023697002320.105120417427-0.02873915090560.0305574229747-0.01779326681610.04614773359380.0642386010712-0.1175110860070.02360520933220.204408727306-0.00266334486530.007762873314310.113802919583-0.009162121926380.1310900928-27.8584674569-42.6136199523-23.8076192284
70.323618522825-0.139234287122-0.08039684628071.17487229790.1529914577650.5527238169540.05128735549570.0436541464455-0.0230015209827-0.0191654987056-0.09249045460250.02939196261430.0327322229229-0.04265983220540.0411474514040.106127459598-0.00680171278131-0.005987189308570.1814129945340.01335192619560.152970903499-17.28782165929.41828904866-54.4662130601
80.515297648732-0.272191484436-0.1243547910621.625366015690.630267206071.026777093990.07709711644580.111131749958-0.0199293471524-0.14828128458-0.0355900116319-0.254567232761-0.002571425929150.0128989093166-0.01351263254150.100605622210.00613580682775-0.002543252312950.1686943877230.03233152123530.191286313705-7.918490893896.29094041754-66.4757181678
90.340316598599-0.14168303139-0.01844251348590.8533829835010.1217065426270.6075937398910.0189163213541-0.00644421596750.05770864290580.0881440697254-0.0251900402796-0.0927297395741-0.03540791409230.006400165909520.004232280700580.13959725343-0.022566734118-0.01301734405190.1756642988290.02593456383620.182995248227-8.8150548861223.9225801571-39.7789505092
101.04469624137-0.530958285302-0.0875320175391.603499223310.1676663687010.8052831844160.0164042438348-0.1233335090660.09792308797330.117528031513-0.05065110504250.0566274492753-0.0731402493355-0.1054500664250.03735228042330.157871780438-0.039237754418-0.007883679393870.1988813140060.01121183212790.180091122803-17.173402537436.8720390819-38.655877549
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 241 )AA0 - 2411 - 242
22chain 'A' and (resid 242 through 308 )AA242 - 308243 - 309
33chain 'A' and (resid 309 through 470 )AA309 - 470310 - 471
44chain 'B' and (resid 0 through 241 )BC0 - 2411 - 242
55chain 'B' and (resid 242 through 308 )BC242 - 308243 - 309
66chain 'B' and (resid 309 through 471 )BC309 - 471310 - 472
77chain 'C' and (resid 0 through 241 )CF0 - 2411 - 242
88chain 'C' and (resid 242 through 471 )CF242 - 471243 - 472
99chain 'D' and (resid 0 through 241 )DH0 - 2411 - 242
1010chain 'D' and (resid 242 through 471 )DH242 - 471243 - 472

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