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- PDB-6smr: A. thaliana serine hydroxymethyltransferase isoform 4 (AtSHMT4) i... -

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Basic information

Entry
Database: PDB / ID: 6smr
TitleA. thaliana serine hydroxymethyltransferase isoform 4 (AtSHMT4) in complex with methotrexate
ComponentsSerine hydroxymethyltransferase 4
KeywordsTRANSFERASE / SHMT / antifolate
Function / homology
Function and homology information


salicylic acid binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / plasmodesma / tetrahydrofolate interconversion / circadian rhythm / pyridoxal phosphate binding / plasma membrane / 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
METHOTREXATE / Chem-PLS / Serine hydroxymethyltransferase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsRuszkowski, M. / Sekula, B. / Dauter, Z.
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
Authors: Ruszkowski, M. / Sekula, B. / Ruszkowska, A. / Contestabile, R. / Nogues, I. / Angelaccio, S. / Szczepaniak, A. / Dauter, Z.
History
DepositionAug 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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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)211,59721
Polymers208,2084
Non-polymers3,38917
Water17,384965
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27560 Å2
ΔGint-99 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.856, 120.975, 131.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 52052.035 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: O23254, glycine hydroxymethyltransferase

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Non-polymers , 5 types, 982 molecules

#2: Chemical
ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N2O8P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 965 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Crystals grew in 80 mM Tris-HCl pH 8.2, 20% PEG3350. Mature crystals were transferred to drops with 80 mM Tris-HCl pH 8.2, 20% PEG3350, 20% ethylene glycol, 50 mM L-serine, and 10 mM MTX. ...Details: Crystals grew in 80 mM Tris-HCl pH 8.2, 20% PEG3350. Mature crystals were transferred to drops with 80 mM Tris-HCl pH 8.2, 20% PEG3350, 20% ethylene glycol, 50 mM L-serine, and 10 mM MTX. After 24-h incubation, crystals were harvested and vitrified in liquid nitrogen.

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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: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→90 Å / Num. obs: 106878 / % possible obs: 98.8 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.108 / Net I/σ(I): 11.6
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 17038 / CC1/2: 0.79 / Rrim(I) all: 0.76 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cd0

6cd0


Resolution: 2.12→88.3 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 24.02
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1068 1 %random
Rwork0.1732 ---
obs0.1738 105720 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.06 Å2 / Biso mean: 38.9 Å2 / Biso min: 16.08 Å2
Refinement stepCycle: final / Resolution: 2.12→88.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14583 0 231 965 15779
Biso mean--57.8 39.29 -
Num. residues----1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONbonds0.00615146
X-RAY DIFFRACTIONangles0.89820490
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)
10.4451-0.06550.1780.7229-0.00221.68170.0968-0.0821-0.0790.06810.03750.07870.1688-0.1763-0.12560.1885-0.0304-0.02930.18410.03850.22819.26633.039356.8442
20.8563-0.35910.39721.7075-0.63231.38850.0425-0.1458-0.15610.06090.17750.29540.2361-0.3103-0.1470.2277-0.0658-0.02940.23920.05390.24672.6344-0.622157.5734
31.8628-0.5436-0.50320.8091-0.31822.14390.1081-0.2821-0.01-0.03290.0171-0.13720.52030.4584-0.08840.46070.0883-0.1290.2509-0.01320.354928.8587-13.725561.1634
40.55790.05250.28761.15820.06191.42940.07240.0325-0.0303-0.05130.0007-0.014-0.0169-0.0057-0.06850.12340.0290.01090.18680.00240.163917.367817.369741.9885
51.18290.24070.93861.221-0.20882.35340.0250.02580.1594-0.0563-0.00070.0673-0.18330.0228-0.00490.15540.03450.05340.1801-0.01470.222317.632420.743734.9818
63.20630.51960.6232.1204-0.46882.10010.004-0.11120.3793-0.06690.11010.4957-0.0958-0.5075-0.11330.28020.0362-0.03960.33970.0210.2898-1.88617.219522.3917
70.56810.0392-0.06610.92140.39491.34170.0308-0.02160.0822-0.0891-0.00070.0554-0.0962-0.0194-0.02310.24880.0717-0.01080.2509-0.03050.25847.65952.72174.6719
84.50931.60742.65684.63571.2835.51640.16640.4498-0.1443-0.4664-0.12750.66030.4276-0.7599-0.11640.2837-0.0036-0.04380.4665-0.06930.3237-9.682441.421468.8432
90.8640.4816-0.01261.53150.06932.0516-0.01640.06550.1851-0.1670.135-0.2788-0.50880.5404-0.07890.3473-0.04590.07780.3659-0.06810.386120.855369.523971.2256
100.5149-0.35720.02391.1320.14580.5131-0.0022-0.11680.02540.04830.0275-0.0117-0.03740.0167-0.02140.20850.041600.2942-0.01870.207616.711739.045289.5188
111.48750.0763-0.47691.2011-0.1061.2097-0.0308-0.1655-0.1550.09640.0747-0.06560.05850.16-0.02710.21620.0777-0.02670.2787-0.01430.220417.142635.849696.2431
121.50410.332-0.51141.8602-0.170.8233-0.0258-0.2835-0.04090.31820.11470.2651-0.064-0.0143-0.08330.34510.09590.04580.38760.06160.2907-2.79237.9759108.4713
135.5692-2.5515-2.60285.94740.02771.7398-0.0209-0.26650.15210.4881-0.1552-0.1468-0.09240.16650.11280.78570.0918-0.24051.1019-0.06071.079928.90377.462766.3747
141.73371.06762.01151.0691-0.30318.113-0.1698-0.17560.454-0.009-0.11030.252-0.5587-0.67350.42191.15750.2169-0.81581.7621-0.171.2884-2.185126.725444.9269
151.1136-2.1009-1.31484.04532.37721.69080.1574-0.0204-0.16070.2315-0.04690.32480.2992-0.2383-0.03350.46070.03250.17060.70650.09830.8447-2.190928.506886.8433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 257 )A0 - 257
2X-RAY DIFFRACTION2chain 'A' and (resid 258 through 332 )A258 - 332
3X-RAY DIFFRACTION3chain 'A' and (resid 333 through 470 )A333 - 470
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 230 )B0 - 230
5X-RAY DIFFRACTION5chain 'B' and (resid 231 through 374 )B231 - 374
6X-RAY DIFFRACTION6chain 'B' and (resid 375 through 470 )B375 - 470
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 257 )C0 - 257
8X-RAY DIFFRACTION8chain 'C' and (resid 258 through 283 )C258 - 283
9X-RAY DIFFRACTION9chain 'C' and (resid 284 through 470 )C284 - 470
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 230 )D0 - 230
11X-RAY DIFFRACTION11chain 'D' and (resid 231 through 374 )D231 - 374
12X-RAY DIFFRACTION12chain 'D' and (resid 375 through 470 )D375 - 470
13X-RAY DIFFRACTION13chain 'A' and (resname MTX)A-2 - 470
14X-RAY DIFFRACTION14chain 'B' and (resname MTX)B0 - 471
15X-RAY DIFFRACTION15chain 'D' and (resname MTX)D0 - 470

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