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- PDB-9sq1: S-Adenosylmethionine synthetase of Thermococcus kodakarensis in c... -

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Basic information

Entry
Database: PDB / ID: 9sq1
TitleS-Adenosylmethionine synthetase of Thermococcus kodakarensis in complex with (S,R)-SAM and PPNP
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / SAM Biosynthesis Stereoselectivity (S / R)-SAM PPNP
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase)
Similarity search - Domain/homology
: / : / (DIPHOSPHONO)AMINOPHOSPHONIC ACID / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsBolz, M. / Gericke, L. / Lukat, P. / Blankenfeldt, W. / Andexer, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Selectivity of Methionine Adenosyltransferases regarding Methionine Enantiomers
Authors: Gericke, L. / Bolz, M. / Haeussler, M. / Kind, K. / Nagel, A. / Brenneisen, J. / Pleiss, J. / Blankenfeldt, W. / Andexer, J.N.
History
DepositionSep 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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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)190,01139
Polymers187,3774
Non-polymers2,63435
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22320 Å2
ΔGint-244 kcal/mol
Surface area55370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.767, 58.995, 236.259
Angle α, β, γ (deg.)90.00, 104.32, 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 / Methionine adenosyltransferase


Mass: 46844.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: mat, TK0545 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: Q5JF22, methionine adenosyltransferase

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Non-polymers , 6 types, 598 molecules

#2: Chemical ChemComp-A1JV3 / (2~{R})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-$l^{3}-sulfanyl]-2-azanyl-butanoic acid / (R,S)-SAM / D-SAM


Mass: 399.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H6NO9P3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% EG, 10% PEG 8k, 0.04 M Li Acetate, 0.1 M Tris Base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.11→114.46 Å / Num. obs: 103091 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.058 / Rrim(I) all: 0.155 / Χ2: 0.83 / Net I/σ(I): 7.6 / Num. measured all: 721846
Reflection shellResolution: 2.11→2.22 Å / % possible obs: 98.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.68 / Num. measured all: 102639 / Num. unique obs: 14892 / CC1/2: 0.956 / Rpim(I) all: 0.278 / Rrim(I) all: 0.736 / Χ2: 0.67 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata processing
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→67.33 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 5229 5.09 %
Rwork0.194 --
obs0.1961 102796 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→67.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12505 0 135 563 13203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212831
X-RAY DIFFRACTIONf_angle_d0.57617404
X-RAY DIFFRACTIONf_dihedral_angle_d4.6291815
X-RAY DIFFRACTIONf_chiral_restr0.0471986
X-RAY DIFFRACTIONf_plane_restr0.0032264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.130.3051620.26453169X-RAY DIFFRACTION99
2.13-2.160.29271800.25783263X-RAY DIFFRACTION99
2.16-2.180.27271850.2483189X-RAY DIFFRACTION97
2.18-2.210.33972020.24673132X-RAY DIFFRACTION98
2.21-2.240.28771830.24273175X-RAY DIFFRACTION97
2.24-2.270.32231600.25543173X-RAY DIFFRACTION96
2.27-2.30.26551690.24493114X-RAY DIFFRACTION96
2.3-2.340.29981670.24263248X-RAY DIFFRACTION99
2.34-2.370.27151670.22583288X-RAY DIFFRACTION99
2.37-2.410.26131540.22593245X-RAY DIFFRACTION99
2.41-2.460.28011780.23343327X-RAY DIFFRACTION99
2.46-2.50.35991750.23783180X-RAY DIFFRACTION99
2.5-2.550.28892010.23163268X-RAY DIFFRACTION99
2.55-2.60.26881770.22753257X-RAY DIFFRACTION100
2.6-2.660.25911900.21723271X-RAY DIFFRACTION99
2.66-2.720.25831830.21413276X-RAY DIFFRACTION99
2.72-2.790.26081690.2123234X-RAY DIFFRACTION99
2.79-2.860.26471380.20943311X-RAY DIFFRACTION100
2.86-2.950.2451600.21213329X-RAY DIFFRACTION99
2.95-3.040.25781760.21373212X-RAY DIFFRACTION99
3.04-3.150.27531830.21863265X-RAY DIFFRACTION99
3.15-3.280.25361710.21993116X-RAY DIFFRACTION94
3.28-3.420.26271590.19773216X-RAY DIFFRACTION98
3.42-3.60.21471870.17533315X-RAY DIFFRACTION99
3.61-3.830.20872190.17373269X-RAY DIFFRACTION99
3.83-4.130.2091520.15513333X-RAY DIFFRACTION100
4.13-4.540.19141590.14473368X-RAY DIFFRACTION100
4.54-5.20.1761820.14013310X-RAY DIFFRACTION100
5.2-6.550.2071360.16493264X-RAY DIFFRACTION95
6.55-67.330.17482050.17793450X-RAY DIFFRACTION100

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