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- PDB-6vd1: Crystal structure of Arabidopsis thaliana S-adenosylmethionine Sy... -

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Basic information

Entry
Database: PDB / ID: 6vd1
TitleCrystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with S-adenosylmethionine and PPNP
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
: / 1,3-PROPANDIOL / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / TRIETHYLENE GLYCOL / R-1,2-PROPANEDIOL / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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)91,43022
Polymers88,3402
Non-polymers3,09020
Water21,5821198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-54 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.205, 101.484, 84.334
Angle α, β, γ (deg.)90.000, 99.370, 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 , 12 types, 1218 molecules

#2: Chemical ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H6NO9P3 / 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-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
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#11: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1198 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
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: 1.32→47.09 Å / Num. obs: 232535 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.35 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.45
Reflection shellResolution: 1.32→1.4 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 37677 / % possible all: 98.2

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Processing

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

6vcz


Resolution: 1.32→47.09 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.023 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 1163 0.5 %RANDOM
Rwork0.1416 ---
obs0.1418 231370 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.77 Å2 / Biso mean: 15.039 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å2-0 Å20.57 Å2
2---1.45 Å20 Å2
3----1.33 Å2
Refinement stepCycle: final / Resolution: 1.32→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 191 1220 7499
Biso mean--24.93 32.3 -
Num. residues----787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136590
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176165
X-RAY DIFFRACTIONr_angle_refined_deg1.811.668941
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5914386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05122.606330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.487151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8291540
X-RAY DIFFRACTIONr_chiral_restr0.1090.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021315
X-RAY DIFFRACTIONr_rigid_bond_restr2.736312755
LS refinement shellResolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 86 -
Rwork0.249 17060 -
all-17146 -
obs--97.79 %

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