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

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Basic information

Entry
Database: PDB / ID: 6vcz
TitleCrystal structure of Arabidopsis thaliana S-adenosylmethionine Synthase 2 (AtMAT2)
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
2-METHOXYETHANOL / TRIETHYLENE GLYCOL / R-1,2-PROPANEDIOL / PHOSPHATE ION / S-adenosylmethionine synthase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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_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.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.ptnr1_symmetry / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,00823
Polymers88,3402
Non-polymers1,66821
Water18,2671014
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-122 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.798, 99.276, 86.930
Angle α, β, γ (deg.)90.000, 109.740, 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 , 7 types, 1035 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1014 / 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: 57.96 %
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 1, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→42.44 Å / Num. obs: 154106 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.26
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 24808 / % possible all: 99.3

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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: 6VCW

6vcw


Resolution: 1.52→42.44 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.46 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 1542 1 %RANDOM
Rwork0.1603 ---
obs0.1605 152562 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.51 Å2 / Biso mean: 20.307 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.35 Å2
2---0.31 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.52→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5868 0 95 1024 6987
Biso mean--33.94 35.05 -
Num. residues----758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0136215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175830
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.6518433
X-RAY DIFFRACTIONr_angle_other_deg1.5521.58613588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.9895.398830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56322.517302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1241535
X-RAY DIFFRACTIONr_chiral_restr0.1110.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021247
LS refinement shellResolution: 1.52→1.558 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.265 113 -
Rwork0.262 11122 -
obs--98.75 %
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)
10.3631-0.15020.07820.2427-0.22750.36190.03080.0994-0.0563-0.0102-0.01590.01690.04450.0228-0.01490.05870.0128-0.010.0545-0.00290.042223.7417.3059.929
20.44890.30040.05911.2941-0.28470.34790.08340.11980.0329-0.0159-0.0420.11830.0134-0.0684-0.04140.04140.0328-0.02260.10720.01450.04049.37512.2492.046
30.34430.0172-0.08930.14470.17450.31610.09580.00750.1159-0.0319-0.06890.0407-0.0886-0.1029-0.02690.05520.01920.02030.06730.02570.099215.52828.1545.884
40.11830.14160.05260.24730.07340.2920.01560.0263-0.0107-0.0197-0.0155-0.0460.03760.0335-0.00010.05030.02310.01230.0616-0.01320.064532.9613.7079.221
50.0679-0.02220.06270.22420.17540.34740.0423-0.0008-0.0555-0.017-0.0217-0.02440.1021-0.0234-0.02060.07440.0136-0.00020.0272-0.00790.100927.938-5.56910.282
60.87740.4110.39980.48650.35490.8123-0.00720.039-0.14130.02290.0269-0.08240.17270.0491-0.01970.06990.0204-0.00050.0114-0.01920.080331.64-11.05611.508
70.1421-0.01060.05020.10320.04690.14240.0150.03980.0079-0.01260.0026-0.02150.00570.0095-0.01760.03940.00220.00910.05790.00150.063430.69614.86214.537
80.5427-0.243-0.16410.22630.22280.24620.07250.09270.0684-0.0563-0.0133-0.0727-0.04280.0143-0.05920.0483-0.00520.0190.06010.04110.069935.37924.2916.934
90.7416-0.19290.07580.0950.02660.05780.03350.14850.006-0.0363-0.0385-0.0015-0.02320.02750.0050.050.00060.03170.09520.0160.037638.2515.7134.319
100.3003-0.0979-0.02850.0753-0.03770.18190.0053-0.0590.0330.00440.0050.02550.0052-0.0451-0.01040.0304-0.0130.01160.0738-0.01070.065610.76813.32326.409
110.3951-0.12610.12480.2804-0.27850.39340.0093-0.093-0.0117-0.02050.01790.07130.0449-0.1107-0.02720.0074-0.01870.00930.101-0.0210.06742.83111.67126.034
120.3332-0.1062-0.02780.15490.05380.3350.0122-0.080.0910.0402-0.017-0.0268-0.03590.01280.00480.0423-0.007-0.00190.0497-0.03320.070724.96430.23933.214
130.18660.0073-0.06010.1280.05450.08920.0149-0.04960.00870.0182-0.0067-0.00750.0357-0.0038-0.00820.0547-0.0002-0.00610.05760.00580.049625.2189.96229.063
140.6936-0.1714-0.11130.42690.49970.60140.0502-0.1854-0.00650.1229-0.0391-0.0180.1585-0.0628-0.01110.0624-0.03550.00050.10260.04690.049523.1080.43837.653
150.6470.08670.33230.15180.18420.3410.0656-0.1315-0.04830.0243-0.06780.01470.033-0.0580.00220.0622-0.03370.00140.14290.02650.013526.3678.51942.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 90
3X-RAY DIFFRACTION3A91 - 123
4X-RAY DIFFRACTION4A124 - 157
5X-RAY DIFFRACTION5A158 - 179
6X-RAY DIFFRACTION6A180 - 232
7X-RAY DIFFRACTION7A233 - 329
8X-RAY DIFFRACTION8A330 - 366
9X-RAY DIFFRACTION9A367 - 389
10X-RAY DIFFRACTION10B1 - 64
11X-RAY DIFFRACTION11B65 - 123
12X-RAY DIFFRACTION12B124 - 232
13X-RAY DIFFRACTION13B233 - 329
14X-RAY DIFFRACTION14B330 - 366
15X-RAY DIFFRACTION15B367 - 391

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