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- PDB-6faj: The structure of Human Methionine Adenosyltransferase II in apo state -

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Basic information

Entry
Database: PDB / ID: 6faj
TitleThe structure of Human Methionine Adenosyltransferase II in apo state
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE
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
GMP Synthetase; Chain A, domain 3 - #10 / 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 ...GMP Synthetase; Chain A, domain 3 - #10 / 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. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBradley-Clarke, J. / Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: Febs J. / Year: 2020
Title: Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory beta subunit and quinolone-based compounds
Authors: Panmanee, J. / Bradley-Clarke, J. / Mato, J.M. / O'Neill, P.M. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,9076
Polymers87,4412
Non-polymers4664
Water5,441302
1
A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
hetero molecules

A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,81412
Polymers174,8834
Non-polymers9318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area15460 Å2
ΔGint-29 kcal/mol
Surface area48630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.176, 103.232, 108.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: 43720.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% PEG600 0.1M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→74.74 Å / Num. obs: 51446 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.937 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.15 / Rrim(I) all: 0.236 / Net I/σ(I): 4.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3573 / CC1/2: 0.845 / Rpim(I) all: 0.322 / Rrim(I) all: 0.506 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A1I

5a1i


Resolution: 1.95→74.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22387 2690 5.2 %RANDOM
Rwork0.18964 ---
obs0.19146 48711 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.511 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2---1.72 Å20 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.95→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5711 0 31 302 6044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195853
X-RAY DIFFRACTIONr_bond_other_d00.025505
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9647914
X-RAY DIFFRACTIONr_angle_other_deg3.737312748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25723.88250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79215990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.171536
X-RAY DIFFRACTIONr_chiral_restr0.0960.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216511
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021165
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_it1.0661.3632961
X-RAY DIFFRACTIONr_mcbond_other1.0651.3622960
X-RAY DIFFRACTIONr_mcangle_it1.8372.0323693
X-RAY DIFFRACTIONr_mcangle_other1.8362.0333694
X-RAY DIFFRACTIONr_scbond_it1.3681.5462892
X-RAY DIFFRACTIONr_scbond_other1.3661.5462892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2572.2414221
X-RAY DIFFRACTIONr_long_range_B_refined3.95516.1086343
X-RAY DIFFRACTIONr_long_range_B_other3.95416.1116344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 193 -
Rwork0.245 3553 -
obs--99.73 %

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