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- PDB-7p82: Crystal structure of apo form L147A/I351A variant of S-adenosylme... -

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Basic information

Entry
Database: PDB / ID: 7p82
TitleCrystal structure of apo form L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii
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
S-adenosylmethionine synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 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


Theoretical massNumber of molelcules
Total (without water)94,8032
Polymers94,8032
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-17 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.641, 75.641, 281.618
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.12 %
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: 2.04→47.96 Å / Num. obs: 59592 / % possible obs: 98.3 % / Redundancy: 16.07 % / CC1/2: 0.997 / Rrim(I) all: 0.165 / Net I/σ(I): 10.99
Reflection shellResolution: 2.04→2.17 Å / Redundancy: 11.77 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 8708 / CC1/2: 0.882 / Rrim(I) all: 0.849 / % possible all: 90.4

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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: 4L7I

4l7i


Resolution: 2.042→47.958 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 2100 3.52 %
Rwork0.2037 57480 -
obs0.2053 59580 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.52 Å2 / Biso mean: 43.53 Å2 / Biso min: 19.07 Å2
Refinement stepCycle: final / Resolution: 2.042→47.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 0 421 6759
Biso mean---44.73 -
Num. residues----813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036423
X-RAY DIFFRACTIONf_angle_d0.6778663
X-RAY DIFFRACTIONf_chiral_restr0.0291005
X-RAY DIFFRACTIONf_plane_restr0.0021120
X-RAY DIFFRACTIONf_dihedral_angle_d11.0142487
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.042-2.08920.3481060.3391292177
2.0892-2.14150.32141400.29343815100
2.1415-2.19940.29591390.27333827100
2.1994-2.26410.26791400.25533830100
2.2641-2.33720.30781410.24323836100
2.3372-2.42070.321400.24663854100
2.4207-2.51760.32921410.22963862100
2.5176-2.63220.25561410.21623843100
2.6322-2.77090.27691410.21963862100
2.7709-2.94450.26461410.22583872100
2.9445-3.17180.24251430.21683917100
3.1718-3.49090.29371430.20773894100
3.4909-3.99590.1971440.18293950100
3.9959-5.03350.2191460.15314003100
5.0335-6.080.20981540.18084194100

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