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- PDB-7p84: Crystal structure of L147A/I351A variant of S-adenosylmethionine ... -

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Basic information

Entry
Database: PDB / ID: 7p84
TitleCrystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine)
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE
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
TRIPHOSPHATE / Chem-EU9 / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsHerrmann, E. / Peters, A. / Cornelissen, N.V. / Rentmeister, A. / Kuemmel, D.
CitationJournal: Chembiochem / Year: 2022
Title: Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases.
Authors: Peters, A. / Herrmann, E. / Cornelissen, N.V. / Klocker, N. / Kummel, D. / Rentmeister, A.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,9128
Polymers94,8032
Non-polymers1,1096
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-55 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.104, 76.104, 280.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 47401.336 Da / Num. of mol.: 2 / Mutation: L147A/I351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: mat, MJ1208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58605, methionine adenosyltransferase
#2: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5O10P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EU9 / [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium


Mass: 520.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N7O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 40% (v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→48.04 Å / Num. obs: 112614 / % possible obs: 99.3 % / Redundancy: 5.59 % / CC1/2: 0.996 / Rrim(I) all: 0.155 / Net I/σ(I): 8.1
Reflection shellResolution: 2.05→2.18 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 17696 / CC1/2: 0.919 / Rrim(I) all: 0.968

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P82

7p82


Resolution: 2.054→48.04 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 2090 1.86 %
Rwork0.1777 110499 -
obs0.1785 112589 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.43 Å2 / Biso mean: 38.66 Å2 / Biso min: 17.74 Å2
Refinement stepCycle: final / Resolution: 2.054→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 86 387 6819
Biso mean--37.42 40.89 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036494
X-RAY DIFFRACTIONf_angle_d0.7758769
X-RAY DIFFRACTIONf_chiral_restr0.0321012
X-RAY DIFFRACTIONf_plane_restr0.0021125
X-RAY DIFFRACTIONf_dihedral_angle_d12.8892514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0541-2.10190.38871300.2931682693
2.1019-2.15450.28361410.27317370100
2.1545-2.21270.30991420.23647384100
2.2127-2.27780.25281400.21157358100
2.2778-2.35130.28121390.20077487100
2.3513-2.43540.23681430.20677383100
2.4354-2.53290.2461390.1887456100
2.5329-2.64820.27011410.18347364100
2.6482-2.78780.21711430.18627427100
2.7878-2.96240.17441390.17447378100
2.9624-3.19110.2451420.1777464100
3.1911-3.51210.19591390.17787367100
3.5121-4.02010.19571390.15767438100
4.0201-5.0640.18191350.13817414100
5.064-6.120.20861380.16397383100

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