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- PDB-7pzz: Crystal structure of serine hydroxymethyltransferase, isoform 2 f... -

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Basic information

Entry
Database: PDB / ID: 7pzz
TitleCrystal structure of serine hydroxymethyltransferase, isoform 2 from Arabidopsis thaliana (SHM2)
ComponentsSerine hydroxymethyltransferase 2, mitochondrial
KeywordsTRANSFERASE / C1 metabolism / tetrahydrofolate / tetramer / PLP-dependent enzyme / mitochondria
Function / homology
Function and homology information


glycine metabolic process / L-serine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / cobalt ion binding / plastid / pyridoxal phosphate binding / mitochondrion / zinc ion 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
DI(HYDROXYETHYL)ETHER / Serine hydroxymethyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2, mitochondrial
B: Serine hydroxymethyltransferase 2, mitochondrial
C: Serine hydroxymethyltransferase 2, mitochondrial
D: Serine hydroxymethyltransferase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,71142
Polymers215,0934
Non-polymers2,61838
Water38,1202116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30920 Å2
ΔGint-106 kcal/mol
Surface area64530 Å2
Unit cell
Length a, b, c (Å)115.201, 131.236, 151.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine hydroxymethyltransferase 2, mitochondrial / AtSHMT2 / Glycine hydroxymethyltransferase 2 / Serine methylase 2


Mass: 53773.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHM2, SHMT2, At5g26780, F2P16.40 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q94C74, glycine hydroxymethyltransferase

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Non-polymers , 6 types, 2154 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2116 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SHM2 15 mg/ml; drop 3+2 uL 90% Index (Hampton Research) F8 (0.2 M Ammonium sulfate, 0.1 M HEPES 7.5, 25% w/v Polyethylene glycol 3,350) cryoprotection with 20% ethylene glycol in the F8 Index condition

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 4, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→80 Å / Num. obs: 274997 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 18.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.19
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 43063 / CC1/2: 0.65 / % possible all: 97

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Processing

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

6smw


Resolution: 1.65→53.84 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1779 1237 0.45 %
Rwork0.1579 273733 -
obs0.158 274970 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7 Å2
Refinement stepCycle: LAST / Resolution: 1.65→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14980 0 160 2116 17256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815502
X-RAY DIFFRACTIONf_angle_d1.008120880
X-RAY DIFFRACTIONf_chiral_restr0.05792265
X-RAY DIFFRACTIONf_plane_restr0.00822690
X-RAY DIFFRACTIONf_dihedral_angle_d13.91675829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.28711310.251529026X-RAY DIFFRACTION95.75
1.71-1.790.27851370.229930270X-RAY DIFFRACTION99.84
1.79-1.880.231370.191130350X-RAY DIFFRACTION99.92
1.88-20.17531380.161130367X-RAY DIFFRACTION99.98
2-2.160.17531370.15630468X-RAY DIFFRACTION99.99
2.16-2.370.21131380.152730468X-RAY DIFFRACTION99.98
2.37-2.720.18411380.155630612X-RAY DIFFRACTION99.96
2.72-3.420.16171390.150430736X-RAY DIFFRACTION99.95
3.42-53.840.14381420.138531436X-RAY DIFFRACTION99.92
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)
10.786695781072-0.410523903670.0491514494390.603095904929-0.1350343386740.6235972921360.0199699772858-0.0127471914487-0.0873536642443-0.009799934857770.008605636600110.06226509527640.04910055427760.00340158550785-0.02527123149420.1305398885630.00508957642654-0.01385639049730.08525829684950.006290767027430.13545014858839.7199705687-19.755276026924.6077803159
20.475849761825-0.2211355619050.06787110378230.566213056203-0.04351365891911.303801224430.0466518969895-0.0352031945932-0.13994142413-0.01878349004850.04401119010090.2052655146420.152288123735-0.115925552138-0.08350645913320.132422478896-0.00854989671557-0.01570884001870.09169243454810.02416848291290.21350887817934.1837954558-26.036200501225.3657069046
32.17488717051-0.70394246469-0.476628373511.699766057920.7502094192252.162326847820.0663857258226-0.18342887590.2835789601830.002048289117010.0853670597739-0.222849593944-0.2061723028090.271589937613-0.1204731012570.1965344166980.01733303860990.01098824864040.2046583943150.01921915783890.17124812622856.828544287-19.544038641845.5946186651
40.536501851645-0.1958407006770.004007640730470.731001312484-0.05753315578380.7155643700830.06026328558110.07220444078360.0162441201733-0.0527950361076-0.0436287663734-0.05794045872440.03761989007780.110877127884-0.01309670596580.1160108387360.0307304997472-0.006039570198370.1214502275830.003742753543750.12081125865953.2088097751-11.92609922817.8067801914
51.257232637590.01879282557580.2363268340972.14644594774-0.2644949675552.390095111540.08288565038540.210921564256-0.140878153288-0.252377212703-0.06711230335910.3636554593440.250459190431-0.21658423279-0.01425049368720.2900459555120.0903032758628-0.04171770750050.278917968425-0.07720463032680.21838948485246.1138386218-30.0972096801-12.4517142161
60.475624874647-0.1901827897790.0008229631573090.6139913752950.002344744817710.4720850462470.04019321206440.03603167161910.0148491221724-0.0386335597872-0.04885676573810.005458723398170.0250070551294-0.02891692147840.004285447427380.114616539360.0292257326857-0.00910069935880.12563086559-0.004153797966360.12183275348917.157788336723.09191218034.74065395097
70.740954547238-0.00690568374648-0.1786454617420.765507180758-0.2347558400560.7054826834190.05452325284850.0956715941791-0.0105595054983-0.126090115968-0.05543510957790.01113961422250.0689038111822-0.00281749224753-0.008729994460630.1174310654660.0514155696428-0.01410819989030.130936682661-0.01994338745210.11449821862516.619326215125.1781444524-3.20937974501
82.81752853932-0.0733573328924-0.4363233331380.4482075929330.098546470161.121052538450.0643962888828-0.05633346898790.222219660293-0.05712694988790.0195206044599-0.123904368869-0.09973615247750.120604312181-0.0933412795110.1817482219740.04904840886070.03038060644940.1363636071810.02769123243570.24827781707429.144834939748.1315147706-2.66022052504
90.56986192561-0.3429285006170.07046588699520.667387581029-0.04164492248580.538774788759-0.0246138472623-0.05706605883950.01647968619930.07159640115640.0125320672970.0117848703320.0198793783213-0.03330114065510.01169550597530.1280915095270.0125559980125-0.0005603858484890.121739651432-0.01513750153540.1298092440216.634996804924.115830109124.4731363011
100.793951420221-0.18286799407-0.241162869760.699817001572-0.2079593143240.831349623171-0.0269129132919-0.098773377636-0.01310622288260.1327832988670.05211331777110.0445916141146-0.016238653486-0.11360831149-0.03234593945180.145562286110.0183244081974-0.02008812257120.128386174447-0.02176263486930.12400161193714.259840997725.048919640832.6131699928
111.74270313530.335341576455-0.1397631962322.43614192334-0.9634926970691.94421721213-0.02605975155730.0314649979393-0.332236355874-0.1607373917770.1641494860210.3936567504130.216647417169-0.447556400204-0.1097648769720.182101059034-0.005511616064620.01157295729870.364312376099-0.009359261001950.30915789222-10.830063612720.52395458932.327033657
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 43 through 272 )AA43 - 2721 - 230
22chain 'A' and (resid 273 through 372 )AA273 - 372231 - 330
33chain 'A' and (resid 373 through 517 )AA373 - 517331 - 475
44chain 'B' and (resid 44 through 372 )BH44 - 3721 - 329
55chain 'B' and (resid 373 through 517 )BH373 - 517330 - 474
66chain 'C' and (resid 43 through 267 )CP43 - 2671 - 225
77chain 'C' and (resid 268 through 408 )CP268 - 408226 - 366
88chain 'C' and (resid 409 through 517 )CP409 - 517367 - 473
99chain 'D' and (resid 38 through 272 )DAA38 - 2721 - 235
1010chain 'D' and (resid 273 through 415 )DAA273 - 415236 - 378
1111chain 'D' and (resid 416 through 517 )DAA416 - 517379 - 480

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