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- PDB-8oog: Crystal structure of human MAT2a with S-Adenosylmethionine and a ... -

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Basic information

Entry
Database: PDB / ID: 8oog
TitleCrystal structure of human MAT2a with S-Adenosylmethionine and a fragment bound in a novel pocket
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / methionine adenosyltransferase / s-adenosylmethionine synthetase / fragment screen / allosteric binder
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion 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
S-ADENOSYLMETHIONINE / 6-oxidanyl-1,3-benzoxathiol-2-one / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.384 Å
AuthorsSchimpl, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2023
Title: Combining structural and coevolution information to unveil allosteric sites.
Authors: La Sala, G. / Pfleger, C. / Kack, H. / Wissler, L. / Nevin, P. / Bohm, K. / Janet, J.P. / Schimpl, M. / Stubbs, C.J. / De Vivo, M. / Tyrchan, C. / Hogner, A. / Gohlke, H. / Frolov, A.I.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6595
Polymers43,9361
Non-polymers7234
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint5 kcal/mol
Surface area15410 Å2
Unit cell
Length a, b, c (Å)67.880, 94.220, 116.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-666-

HOH

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Components

#1: Protein S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43935.828 Da / Num. of mol.: 1 / Fragment: full length protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-VUO / 6-oxidanyl-1,3-benzoxathiol-2-one


Mass: 168.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 8 % PEG8000, 12 % ethylene glycol, 0.1 M Hepes pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.384→73.374 Å / Num. obs: 75517 / % possible obs: 98.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Net I/σ(I): 13.3 / Num. measured all: 466961
Reflection shellResolution: 1.384→1.408 Å / % possible obs: 97.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 1.097 / Num. measured all: 23485 / Num. unique obs: 3671 / Rpim(I) all: 0.466 / Rrim(I) all: 1.194 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.11.8 (24-FEB-2021)refinement
Aimlessdata scaling
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.384→73.37 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.057
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 3763 4.98 %RANDOM
Rwork0.19 ---
obs0.1905 75517 98.7 %-
Displacement parametersBiso mean: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1--4.8154 Å20 Å20 Å2
2--1.3769 Å20 Å2
3---3.4385 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.384→73.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 46 176 3164
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083048HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14130HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1057SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3048HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.61
X-RAY DIFFRACTIONt_other_torsion14.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion392SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2848SEMIHARMONIC4
LS refinement shellResolution: 1.384→1.39 Å
RfactorNum. reflection% reflection
Rfree0.2466 -4.9 %
Rwork0.275 1437 -
obs--97.4 %
Refinement TLS params.Method: refined / Origin x: 26.0243 Å / Origin y: 38.907 Å / Origin z: 32.6625 Å
111213212223313233
T0.0327 Å2-0.0065 Å2-0.0061 Å2--0.0165 Å2-0.0005 Å2---0.0293 Å2
L0.1428 °2-0.1045 °20.0382 °2-0.3398 °20.0012 °2--0.208 °2
S0.0017 Å °0.0012 Å °-0.0207 Å °-0.0443 Å °0.0098 Å °0.0329 Å °0.024 Å °-0.0258 Å °-0.0115 Å °
Refinement TLS groupSelection details: { A|* }

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