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- PDB-6vd2: Crystal structure of Arabidopsis thaliana S-adenosylmethionine Sy... -

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Basic information

Entry
Database: PDB / ID: 6vd2
TitleCrystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine
ComponentsS-adenosylmethionine synthase 2
KeywordsTRANSFERASE / methionine adenosyltransferase / SAM synthase
Function / homology
Function and homology information


plant-type cell wall / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / plasmodesma / one-carbon metabolic process / copper ion binding / nucleolus / extracellular exosome / ATP binding / cytosol
Similarity search - Function
S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
: / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSekula, B. / Ruszkowski, M. / Dauter, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)The Intramural Research Program United States
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
Authors: Sekula, B. / Ruszkowski, M. / Dauter, Z.
History
DepositionDec 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase 2
B: S-adenosylmethionine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,93821
Polymers88,3402
Non-polymers2,59919
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-67 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.980, 101.354, 84.708
Angle α, β, γ (deg.)90.000, 99.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein S-adenosylmethionine synthase 2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2


Mass: 44169.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SAM2, At4g01850, T7B11.11 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17562, methionine adenosyltransferase

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Non-polymers , 9 types, 635 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Alcohols (1,6-hexanediol; 1-butanol; 1,2-propanediol; 2-propanol; 1,4-butanediol; 1,3-propanediol), 0.1 M HEPES and MOPS buffer at pH 7.5, 20% mmPEG500, 10% PEG 20000

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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: Aug 17, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→45.72 Å / Num. obs: 71629 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.21 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.7
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 11496 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VCZ

6vcz


Resolution: 1.97→45.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.591 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 1075 1.5 %RANDOM
Rwork0.1912 ---
obs0.1919 70546 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.49 Å2 / Biso mean: 35.771 Å2 / Biso min: 19.38 Å2
Baniso -1Baniso -2Baniso -3
1-5.86 Å20 Å21.33 Å2
2---3.06 Å20 Å2
3----3.07 Å2
Refinement stepCycle: final / Resolution: 1.97→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 160 616 6856
Biso mean--46.97 44.09 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175936
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.6518648
X-RAY DIFFRACTIONr_angle_other_deg1.3991.58413817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61622.532316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.925151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3611538
X-RAY DIFFRACTIONr_chiral_restr0.0920.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
LS refinement shellResolution: 1.97→2.017 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 78 -
Rwork0.332 5108 -
obs--95.75 %
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)
10.04480.0982-0.01580.6431-0.58250.7087-0.02210.01960.0549-0.1890.09080.160.1725-0.0614-0.06870.1062-0.0123-0.11270.04280.01610.152915.061910.75138.0095
20.00360.0197-0.00110.2256-0.18450.5113-0.0057-0.00970.0125-0.101-0.06170.01120.06670.07060.06740.06570.0132-0.04020.0665-0.00490.099332.61316.631911.6369
30.52230.00030.22390.52850.52241.66420.09430.11830.0115-0.1474-0.1333-0.0025-0.19450.05320.0390.12270.0123-0.05950.09670.04530.064535.560224.7996.1721
44.19822.21960.84111.6240.7350.4026-0.1184-0.0988-0.3554-0.3734-0.0098-0.0506-0.20370.04490.12820.20290.0157-0.05010.07310.10920.206643.077817.08353.1287
50.2499-0.16790.02460.3299-0.34250.49790.0763-0.0462-0.0243-0.01320.06080.1209-0.049-0.06-0.13720.0451-0.0296-0.01830.07240.00890.161211.782913.036429.0503
60.03010.0383-0.12130.2117-0.21740.53240.0239-0.0196-0.020.0436-0.05870.0455-0.04880.07370.03480.056-0.0316-0.05220.0776-0.01590.119929.199117.186631.3331
70.9665-0.1145-0.38240.07220.2171.1847-0.0271-0.24790.09270.0685-0.0485-0.03550.24150.04340.07560.0849-0.0564-0.02010.14510.04490.110130.3932-0.954837.5413
81.7287-0.2859-0.10310.0756-0.04260.758-0.03830.0046-0.15050.0681-0.08320.029-0.05710.25960.12150.1948-0.10890.00660.14580.02060.065534.17467.129542.0833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 329
3X-RAY DIFFRACTION3A330 - 366
4X-RAY DIFFRACTION4A367 - 394
5X-RAY DIFFRACTION5B0 - 100
6X-RAY DIFFRACTION6B101 - 329
7X-RAY DIFFRACTION7B330 - 366
8X-RAY DIFFRACTION8B367 - 391

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