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- PDB-8jzi: Mutant S-adenosylmethionine synthase from C. glutamicum -

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Basic information

Entry
Database: PDB / ID: 8jzi
TitleMutant S-adenosylmethionine synthase from C. glutamicum
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 / cytoplasm
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
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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)177,57116
Polymers176,6704
Non-polymers90212
Water22,0141222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-94 kcal/mol
Surface area48880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.404, 125.436, 116.310
Angle α, β, γ (deg.)90.00, 128.91, 90.00
Int Tables number5
Space group name H-MC121

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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: 44167.398 Da / Num. of mol.: 4 / Mutation: E68A
Source method: isolated from a genetically manipulated source
Details: His-tag: LEHHHHHH (410-407) invisible region chain A : 103 - 126 invisible region chain B : 104 - 131 invisible region chain C : 103 - 128 invisible region chain D : 103 - 127
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 , 5 types, 1234 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, MES pH 6.5

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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: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 164669 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.814 / CC star: 0.947 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.137 / Rrim(I) all: 0.265 / Χ2: 15.62 / Net I/σ(I): 12.1 / Num. measured all: 605841
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.76-1.793.10.34578320.8120.9470.2250.4143.16594.9
1.79-1.823.60.34982000.850.9590.2150.4113.52799.5
1.82-1.863.70.34682530.8320.9530.2090.4044.00599.6
1.86-1.93.70.3282150.870.9650.1930.3744.64399.6
1.9-1.943.70.29182250.8640.9630.1750.345.32199.7
1.94-1.983.70.27682520.8850.9690.1660.3235.93599.8
1.98-2.033.70.2682550.8740.9660.1570.3047.25699.8
2.03-2.093.80.24582800.880.9680.1470.2867.8399.8
2.09-2.153.80.23982140.8720.9650.1430.2798.92699.9
2.15-2.223.80.23582580.8770.9670.140.27410.07199.9
2.22-2.33.80.23182860.8790.9670.1370.26911.586100
2.3-2.393.80.22682630.880.9670.1350.26412.904100
2.39-2.53.80.22982720.870.9640.1360.26614.529100
2.5-2.633.80.22582860.880.9680.1340.26215.63100
2.63-2.793.80.2282860.890.9710.1310.25617.889100
2.79-3.013.80.21982800.8560.960.130.25421.643100
3.01-3.313.80.21682950.8910.9710.1290.25228.474100
3.31-3.793.70.21883100.8330.9530.1310.25538.70199.7
3.79-4.783.50.21881950.8240.950.1350.25647.23998.5
4.78-503.40.21682120.8070.9450.1360.25646.18597.3

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Processing

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

3tde


Resolution: 1.76→31.55 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.33 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 8140 4.9 %RANDOM
Rwork0.18216 ---
obs0.18393 156528 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.35 Å2
2--0.53 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.76→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11691 0 56 1222 12969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311944
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511425
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.64116221
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5826249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66251521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66221.473638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.477151948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.05515103
X-RAY DIFFRACTIONr_chiral_restr0.0850.21598
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022648
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_it1.7731.8956108
X-RAY DIFFRACTIONr_mcbond_other1.7721.8946107
X-RAY DIFFRACTIONr_mcangle_it2.5012.8317621
X-RAY DIFFRACTIONr_mcangle_other2.5012.8317622
X-RAY DIFFRACTIONr_scbond_it2.5112.1895836
X-RAY DIFFRACTIONr_scbond_other2.512.1895837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7723.1788601
X-RAY DIFFRACTIONr_long_range_B_refined5.4823.85413396
X-RAY DIFFRACTIONr_long_range_B_other5.38123.45813133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å
RfactorNum. reflection% reflection
Rfree0.281 595 -
Rwork0.225 10923 -
obs--94.06 %

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