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

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Basic information

Entry
Database: PDB / ID: 6vcx
TitleCrystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 1 (AtMAT1)
ComponentsS-adenosylmethionine synthase 1
KeywordsTRANSFERASE / methionine adenosyltransferase / SAM synthase
Function / homology
Function and homology information


ethylene biosynthetic process / plant-type cell wall / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / extracellular region / ATP binding / metal ion 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
S-adenosylmethionine synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.2Apr 3, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,31715
Polymers43,4871
Non-polymers83014
Water9,728540
1
A: S-adenosylmethionine synthase 1
hetero molecules

A: S-adenosylmethionine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,63430
Polymers86,9742
Non-polymers1,65928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area9130 Å2
ΔGint-256 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.722, 68.096, 209.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1-

MET

21A-542-

HOH

31A-643-

HOH

41A-971-

HOH

51A-1036-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43487.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: leaves / Gene: SAM1, At1g02500, T14P4.17, T14P4_22 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23686, methionine adenosyltransferase

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Non-polymers , 5 types, 554 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.8 M (NH4)2SO4, 0.08 M Bis-Tris

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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: May 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: 1.1→48.78 Å / Num. obs: 160169 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 7.38 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.51
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 7.36 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.91 / Num. unique obs: 24752 / % possible all: 92.8

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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: D_1000245963

Resolution: 1.1→48.78 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.693 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.023
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1353 1602 1 %RANDOM
Rwork0.1106 ---
obs0.1109 158566 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.55 Å2 / Biso mean: 13.017 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---0.02 Å20 Å2
3---1.14 Å2
Refinement stepCycle: final / Resolution: 1.1→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 41 551 3567
Biso mean--19.84 28.09 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133263
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173063
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6534454
X-RAY DIFFRACTIONr_angle_other_deg1.5771.5857169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42423.106161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15615581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0681518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023679
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02643
X-RAY DIFFRACTIONr_rigid_bond_restr4.72736324
LS refinement shellResolution: 1.101→1.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 112 -
Rwork0.167 11069 -
all-11181 -
obs--91.49 %

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