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- PDB-8jzg: C. glutamicum S-adenosylmethionine synthase co-crystallized with ... -

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Basic information

Entry
Database: PDB / ID: 8jzg
TitleC. glutamicum S-adenosylmethionine synthase co-crystallized with Adenosine, triphosphate, and SAM
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosylmethionine synthase / complex / SAM
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / 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
TRIPHOSPHATE / ADENOSINE / : / PYROPHOSPHATE 2- / S-ADENOSYLMETHIONINE / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLee, S. / Kim, K.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021M3D3A1A01079480_2021-5 Korea, Republic Of
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum .
Authors: Lee, S. / Kim, S. / Kim, I.K. / Kim, K.J.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,30731
Polymers176,9024
Non-polymers4,40627
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24460 Å2
ΔGint-128 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.311, 116.806, 116.314
Angle α, β, γ (deg.)90.00, 103.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 44225.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tag: LEHHHHHH (410-417) invisible region chain A : 102 -125 invisible region chain B : 103 -126 invisible region chain C : 102 -126 invisible region chain D : 103 -125
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: metK, Cgl1603, cg1806 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K5E4, methionine adenosyltransferase

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Non-polymers , 8 types, 310 molecules

#2: Chemical
ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium phosphate monobasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 62235 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.048 / Rrim(I) all: 0.093 / Χ2: 1.888 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.20.35930830.7810.9370.2350.4321.46299.1
2.44-2.493.20.32730940.8210.950.2140.3921.41398.8
2.49-2.533.20.29630780.8710.9650.1910.3541.47899.1
2.53-2.593.30.2830790.8810.9680.1810.3351.50798.7
2.59-2.643.30.24231010.9040.9740.1540.2891.50199
2.64-2.73.40.21430920.9380.9840.1360.2551.63199
2.7-2.773.40.20430970.9420.9850.1280.2411.63499.3
2.77-2.853.40.18330750.9520.9880.1140.2171.64599.3
2.85-2.933.40.16231510.9680.9920.10.1911.65799.5
2.93-3.023.50.14530570.9680.9920.0890.1711.74999.2
3.02-3.133.60.12531200.9820.9950.0760.1471.80899.4
3.13-3.263.70.10631240.9870.9970.0630.1241.83499.6
3.26-3.413.80.08931150.990.9970.0520.1031.92999.7
3.41-3.583.90.07531240.9930.9980.0430.0871.98699.8
3.58-3.813.90.06831130.9940.9990.0390.0792.09899.9
3.81-4.13.90.05931660.9960.9990.0330.0682.17299.8
4.1-4.523.90.05331060.9950.9990.030.0612.29199.6
4.52-5.173.90.04931500.9960.9990.0280.0572.26199.7
5.17-6.513.90.05131480.9960.9990.0290.0592.21599.7
6.51-503.70.04831620.9950.9990.0290.0562.81198.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TDE

3tde


Resolution: 2.39→32.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.18 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.511 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 3194 5.1 %RANDOM
Rwork0.19374 ---
obs0.1983 59022 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.026 Å2
Baniso -1Baniso -2Baniso -3
1-4.39 Å2-0 Å2-0.51 Å2
2---0.08 Å2-0 Å2
3----3.66 Å2
Refinement stepCycle: 1 / Resolution: 2.39→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11853 0 269 283 12405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312327
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511629
X-RAY DIFFRACTIONr_angle_refined_deg1.71.64616786
X-RAY DIFFRACTIONr_angle_other_deg1.2491.58226728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60151540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01421.646656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.062151979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.56215104
X-RAY DIFFRACTIONr_chiral_restr0.0710.21656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4934.2096196
X-RAY DIFFRACTIONr_mcbond_other3.4934.2096196
X-RAY DIFFRACTIONr_mcangle_it5.3036.2947724
X-RAY DIFFRACTIONr_mcangle_other5.3036.2947725
X-RAY DIFFRACTIONr_scbond_it3.5324.5566131
X-RAY DIFFRACTIONr_scbond_other3.5324.5566131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4726.7099063
X-RAY DIFFRACTIONr_long_range_B_refined8.2349.73313270
X-RAY DIFFRACTIONr_long_range_B_other8.23249.73513262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.393→2.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 256 -
Rwork0.28 4070 -
obs--92.67 %

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