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- PDB-7loz: S-adenosylmethionine synthetase -

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Basic information

Entry
Database: PDB / ID: 7loz
TitleS-adenosylmethionine synthetase
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / S-adenosylmethionine synthetase
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm
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
PHOSPHATE ION / PYROPHOSPHATE 2- / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEscherichia coli 908573 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTan, L.L. / Jackson, C.J.
CitationJournal: Jacs Au / Year: 2021
Title: Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases.
Authors: Gade, M. / Tan, L.L. / Damry, A.M. / Sandhu, M. / Brock, J.S. / Delaney, A. / Villar-Briones, A. / Jackson, C.J. / Laurino, P.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,74817
Polymers85,6092
Non-polymers1,13915
Water2,828157
1
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules

A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,49634
Polymers171,2184
Non-polymers2,27930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area20880 Å2
ΔGint-162 kcal/mol
Surface area50390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.600, 122.600, 288.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42804.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

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Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.74 Å3/Da / Density % sol: 67.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris 6.5, 15% ethylene glycol, PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→39.75 Å / Num. obs: 61889 / % possible obs: 100 % / Redundancy: 30.3 % / Biso Wilson estimate: 57.01 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.2
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 4507 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PL7

1pl7


Resolution: 2.25→39.09 Å / SU ML: 0.2695 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 3066 4.97 %
Rwork0.1896 58563 -
obs0.1906 61629 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.47 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5884 0 62 157 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576092
X-RAY DIFFRACTIONf_angle_d0.79518265
X-RAY DIFFRACTIONf_chiral_restr0.052918
X-RAY DIFFRACTIONf_plane_restr0.00521078
X-RAY DIFFRACTIONf_dihedral_angle_d17.05152236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.31051380.31042619X-RAY DIFFRACTION99.96
2.29-2.320.35151540.28322594X-RAY DIFFRACTION99.96
2.32-2.360.30441500.2732605X-RAY DIFFRACTION100
2.36-2.410.31061290.25872615X-RAY DIFFRACTION99.96
2.41-2.450.27861250.24532632X-RAY DIFFRACTION99.89
2.45-2.50.27661380.2432603X-RAY DIFFRACTION99.96
2.5-2.560.24881490.23062630X-RAY DIFFRACTION99.93
2.56-2.620.22641370.20752605X-RAY DIFFRACTION100
2.62-2.680.24581320.20752619X-RAY DIFFRACTION99.96
2.68-2.750.23971260.20552633X-RAY DIFFRACTION99.96
2.75-2.830.25851460.20272620X-RAY DIFFRACTION99.96
2.83-2.930.22941300.20062651X-RAY DIFFRACTION99.89
2.93-3.030.24011340.1952650X-RAY DIFFRACTION100
3.03-3.150.21171230.19132660X-RAY DIFFRACTION100
3.15-3.30.2061300.19012665X-RAY DIFFRACTION100
3.3-3.470.21461300.18122672X-RAY DIFFRACTION100
3.47-3.690.19131480.18182666X-RAY DIFFRACTION100
3.69-3.970.20921400.17032687X-RAY DIFFRACTION100
3.97-4.370.18611360.1672711X-RAY DIFFRACTION100
4.37-50.18651440.15842722X-RAY DIFFRACTION99.97
5-6.30.19011740.19382752X-RAY DIFFRACTION100
6.3-39.090.20051530.19282952X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.404239012-0.0011128068120.08695557427891.361866315880.1889490023290.874284223798-0.0891930800125-0.1904056968350.07092856069750.438276125835-0.1630696293790.0460925456326-0.0949516457501-0.07934716542350.2587816023310.572796494182-0.0922379325853-0.09017689413680.4902116946310.1158940492680.404867647378-28.4010425059-39.808913393-16.1296345131
23.805594400282.903524016513.178952810762.232871911732.43361809232.68179777724-0.01279549877680.46243327377-0.3156234960190.4984446222030.387938262876-0.640729413949-0.1471109577930.504639398626-0.1915351714010.79145547539-0.05580740264-0.05068303423220.521031668320.08165601512990.599245948704-13.0156872455-48.148668153-8.78959048831
31.63780973750.07528040911610.4980702100090.5347043952060.1114701127430.711787731585-0.1916031242050.03538006543110.3406456798830.288520209950.086480089243-0.0616170397938-0.126592803318-0.01860626192340.08966160815760.658522284898-0.0369511446704-0.1861444460830.4357067399720.09971922046560.553509157366-19.7414282577-22.106648888-18.566191271
40.776406694841-0.4689137852330.669664456571.31477417460.1052754555891.55994109414-0.3400646307180.1527466442430.05070615204470.4041550949320.386915234014-0.544521581813-0.5255859122290.56154450444-0.04004917562410.682792528734-0.0741344581908-0.03238291248040.7457038403170.2346564209380.705234271096-3.66395883026-37.3265314992-26.2939836282
52.32661196244-0.1618864446010.6449142893572.25028843385-1.362851304422.73726404842-0.3687979377910.226728268188-0.312115694381-0.388913011605-0.269291280236-0.5510724991060.5050843861690.345495397430.6069892744240.5798451295420.0002067247516970.1724385402870.5758517267320.1518781729150.610757307691-17.2886881787-53.2505703345-35.1382621355
60.3569402886061.3269486945-1.163261686114.97718757994-4.372478170723.8380896228-0.154996976160.362562375920.3687414258810.07172429531860.7214738867140.991898072686-0.454663319228-0.332415277671-0.1915744274530.742608179017-0.1080909285190.07884907318880.6640865657140.1389498598630.821256536085-31.9872190363-39.8593169239-42.1550732544
70.7181118925280.06479655011450.1530784515781.7643294633-0.1682985517570.977686479339-0.1784708774390.1969828637330.09982052949150.182494760943-0.102086995838-0.6539298354160.05859239066210.4641712879010.2203167099260.517393251665-0.110887847152-0.113920955770.791307355910.2876579660320.759919878104-3.88689666169-32.8886565963-34.7096705484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 383 )
4X-RAY DIFFRACTION4chain 'B' and (resid -7 through 31 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 89 )
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 110 )
7X-RAY DIFFRACTION7chain 'B' and (resid 111 through 382 )

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