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- PDB-7low: S-adenosylmethionine synthetase -

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Basic information

Entry
Database: PDB / ID: 7low
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: 2.39 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 10, 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)86,81018
Polymers85,6092
Non-polymers1,20116
Water2,396133
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)173,62136
Polymers171,2184
Non-polymers2,40332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area20650 Å2
ΔGint-161 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.954, 122.954, 288.087
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

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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, 149 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.5, 15% ethylene glycol, 20% PEG 3350

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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: 2.39→39.86 Å / Num. obs: 51892 / % possible obs: 100 % / Redundancy: 39.4 % / Biso Wilson estimate: 58.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.5
Reflection shellResolution: 2.39→2.46 Å / Num. unique obs: 4416 / CC1/2: 0.434

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Processing

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

1pl7


Resolution: 2.39→39.1 Å / SU ML: 0.3037 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 2636 5.09 %
Rwork0.1823 49148 -
obs0.184 51784 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.36 Å2
Refinement stepCycle: LAST / Resolution: 2.39→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 66 133 6012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346000
X-RAY DIFFRACTIONf_angle_d0.60438130
X-RAY DIFFRACTIONf_chiral_restr0.0464903
X-RAY DIFFRACTIONf_plane_restr0.00411055
X-RAY DIFFRACTIONf_dihedral_angle_d15.97392192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.430.32881410.30222519X-RAY DIFFRACTION100
2.43-2.480.34581250.31042555X-RAY DIFFRACTION99.96
2.48-2.530.34421260.29282528X-RAY DIFFRACTION99.92
2.53-2.590.27151230.26172555X-RAY DIFFRACTION100
2.59-2.650.31611490.24882524X-RAY DIFFRACTION100
2.65-2.710.28091330.23642546X-RAY DIFFRACTION100
2.71-2.790.27611450.23232542X-RAY DIFFRACTION100
2.79-2.870.2481340.21842555X-RAY DIFFRACTION100
2.87-2.960.25421360.20942564X-RAY DIFFRACTION100
2.96-3.070.24041320.2022560X-RAY DIFFRACTION100
3.07-3.190.22271560.18962542X-RAY DIFFRACTION100
3.19-3.330.21751460.18152577X-RAY DIFFRACTION100
3.33-3.510.20361220.17912589X-RAY DIFFRACTION100
3.51-3.730.21821460.16522593X-RAY DIFFRACTION99.96
3.73-4.020.17541430.15532589X-RAY DIFFRACTION100
4.02-4.420.17941320.15012624X-RAY DIFFRACTION100
4.42-5.060.16541370.14472648X-RAY DIFFRACTION99.96
5.06-6.370.19091710.18392657X-RAY DIFFRACTION100
6.37-39.10.24071390.17612881X-RAY DIFFRACTION99.7
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)
12.08521146190.07533686915980.226795571481.86387325235-0.06463021250121.57124134069-0.0971814019405-0.21285845320.162863727130.350251243431-0.1803108350270.0445997976112-0.0609213321252-0.13267181790.2238981119030.500591976469-0.0799236313515-0.08238271650460.4190681386450.06511033201420.336565620678-28.7379438029-39.8671425299-16.0622296806
22.228151177981.331046857170.9937645934711.094058785460.8064658291010.5976842999890.0397554166184-0.0877736886676-0.3567497596190.5423472472590.14818330024-0.591470022458-0.05485845855260.187828984091-0.1333665241110.839490717765-0.0708906104349-0.153532858240.465310346490.06629645946910.580798709242-9.92380751928-43.9915430851-8.05538037038
32.27574130281-0.6144207029090.4196446091441.72600308668-0.2860040396571.40507123469-0.2297885046180.1679251343460.3435517467070.2635717470150.0804923334307-0.020460586924-0.176462861548-0.09285306108720.1327014922590.588676115088-0.0426058234357-0.1463952523920.4511654079410.0957343744350.537122962819-29.105487657-21.8889529688-25.6677841141
41.031650390850.4012765962960.7681945126242.28031606657-0.1449251685351.22029083365-0.18891856832-0.0734893612330.4954216396230.2811448065870.0242651335725-0.177563350958-0.2456981841780.02594736686390.1465039723770.742443124715-0.00793536953675-0.2481829176590.4544305704030.02466199978060.627233235764-9.26892709836-21.7442695639-9.84557987168
53.568741322762.09805405093.474909986441.745832902242.470910270553.72701202194-0.4716363791270.1064656175230.2349774915090.1696468883060.3571597621-0.286423373896-0.7047280885210.5721656819390.4290579157170.708597420183-0.115377177684-0.06378267938360.6719724950520.1797536944490.654320117864-3.63141220724-37.3373663069-26.0063133304
63.26105191634-0.2711510506660.8001869718042.96443925537-1.974499712544.08579316362-0.266212341650.240977654271-0.21822748358-0.461995569386-0.278758347308-0.49689648570.5901547654810.3905036724720.4979034488940.560863099508-0.01595302274620.1427046067440.5207793253890.1044860316810.500450111684-17.5367873467-53.269156588-35.0382425166
70.105385094112-0.5040173963560.166659255923.27519026376-1.571007966320.886252650823-0.2032666231770.3081750411910.114068698284-0.217048804240.3950040961640.677179582042-0.179919334153-0.0532156080477-0.3589645066130.54123430729-0.119753677849-0.04255046720430.7330459933680.1703599985210.633212644896-28.6524389064-36.4602191668-42.8364435289
80.6090006745520.04604979512170.04380047268921.91255566141-0.247576096621.08113839358-0.1597048449320.2476546540040.2231434637040.15964558647-0.144035927248-0.590471100730.003820769568960.414576226130.2929046377590.500133819458-0.10466171896-0.1066575278990.7384000582510.2589759552680.726596878958-3.40561898734-33.0133449006-34.3348091532
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 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 269 )
4X-RAY DIFFRACTION4chain 'A' and (resid 270 through 382 )
5X-RAY DIFFRACTION5chain 'B' and (resid -8 through 31 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 89 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 119 )
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 382 )

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