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- PDB-6vd0: Crystal structure of Arabidopsis thaliana S-adenosylmethionine Sy... -

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Basic information

Entry
Database: PDB / ID: 6vd0
TitleCrystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2) in complex with free Methionine and AMPCPP
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
GMP Synthetase; Chain A, domain 3 - #10 / 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 ...GMP Synthetase; Chain A, domain 3 - #10 / 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. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / METHIONINE / DI(HYDROXYETHYL)ETHER / S-adenosylmethionine synthase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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
C: S-adenosylmethionine synthase 2
D: S-adenosylmethionine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,91632
Polymers176,6804
Non-polymers4,23628
Water21,6181200
1
A: S-adenosylmethionine synthase 2
B: S-adenosylmethionine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,47917
Polymers88,3402
Non-polymers2,13915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-61 kcal/mol
Surface area25580 Å2
MethodPISA
2
C: S-adenosylmethionine synthase 2
D: S-adenosylmethionine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,43715
Polymers88,3402
Non-polymers2,09713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-70 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.941, 84.721, 119.503
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 388
2010B1 - 388
1020A1 - 387
2020C1 - 387
1030A1 - 389
2030D1 - 389
1040B1 - 387
2040C1 - 387
1050B1 - 388
2050D1 - 388
1060C1 - 387
2060D1 - 387

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 44169.883 Da / Num. of mol.: 4
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 , 8 types, 1228 molecules

#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 16, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.83 Å / Num. obs: 136621 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.21 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 8.78
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 13511 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VCZ

6vcz


Resolution: 2→39.83 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.462 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 2672 2 %RANDOM
Rwork0.222 ---
obs0.2226 133001 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.88 Å2 / Biso mean: 26.208 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.09 Å2
2--0.08 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12053 0 252 1201 13506
Biso mean--29.93 32.8 -
Num. residues----1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312610
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711638
X-RAY DIFFRACTIONr_angle_refined_deg1.661.65317104
X-RAY DIFFRACTIONr_angle_other_deg1.3531.58427076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16851570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74322.567635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52152107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3761576
X-RAY DIFFRACTIONr_chiral_restr0.0850.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022545
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128720.05
12B128720.05
21A128900.06
22C128900.06
31A129890.05
32D129890.05
41B128880.06
42C128880.06
51B129700.05
52D129700.05
61C129250.05
62D129250.05
LS refinement shellResolution: 2→2.048 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.287 185 -
Rwork0.264 8545 -
obs--86.43 %
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)
10.1749-0.17310.01330.2351-0.02270.0079-0.0142-0.001-0.0630.01240.01770.03510.00280.0056-0.00350.00470.0060.01210.0173-0.00330.096523.93743.036-0.432
20.3034-0.162-0.02450.1998-0.01460.01210.00270.0090.07880.01970.0041-0.0229-0.008-0.0056-0.00680.00680.00310.00820.0038-0.0070.101527.09765.9310.026
30.1586-0.14490.00890.2432-0.03680.0111-0.00520.006-0.0680.00080.00570.03090.00820.0007-0.00050.02980.0021-0.00220.006-0.01160.058618.27625.08858.556
40.2047-0.1042-0.05310.1942-0.01120.02580.0246-0.00270.0409-0.0006-0.01440.0057-0.0130.0068-0.01010.0169-0.0025-0.00610.00550.0040.058220.8747.9159.474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 392
2X-RAY DIFFRACTION2B1 - 389
3X-RAY DIFFRACTION3C1 - 389
4X-RAY DIFFRACTION4D1 - 388

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