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- PDB-7ll3: S-adenosylmethionine synthetase co-crystallized with UppNHp -

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Basic information

Entry
Database: PDB / ID: 7ll3
TitleS-adenosylmethionine synthetase co-crystallized with UppNHp
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
(DIPHOSPHONO)AMINOPHOSPHONIC ACID / Chem-UNP / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEscherichia coli 908573 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 3, 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)85,35312
Polymers83,9972
Non-polymers1,35610
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)170,70624
Polymers167,9944
Non-polymers2,71220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area17540 Å2
ΔGint-90 kcal/mol
Surface area51660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.655, 123.655, 289.409
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-870-

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: 41998.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Plasmid: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

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Non-polymers , 5 types, 143 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UNP / 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PPK / (DIPHOSPHONO)AMINOPHOSPHONIC ACID


Mass: 256.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H6NO9P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: 3.8 Å3/Da / Density % sol: 67.65 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 8000, 0.1 M Bis-Tris pH 6.5, 20% ethylene glycol

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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: 2.24→43.98 Å / Num. obs: 63722 / % possible obs: 100 % / Redundancy: 32.8 % / Biso Wilson estimate: 67.56 Å2 / CC1/2: 1 / Net I/σ(I): 19.6
Reflection shellResolution: 2.24→2.3 Å / Num. unique obs: 4401 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p7L

1p7l


Resolution: 2.24→43.98 Å / SU ML: 0.3383 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 3190 5.02 %
Rwork0.2114 60390 -
obs0.2126 63580 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.25 Å2
Refinement stepCycle: LAST / Resolution: 2.24→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5795 0 77 133 6005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046052
X-RAY DIFFRACTIONf_angle_d0.58778220
X-RAY DIFFRACTIONf_chiral_restr0.0451911
X-RAY DIFFRACTIONf_plane_restr0.00431068
X-RAY DIFFRACTIONf_dihedral_angle_d18.04952246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.40861160.37982574X-RAY DIFFRACTION99.93
2.27-2.310.41171360.3412591X-RAY DIFFRACTION100
2.31-2.350.31651420.30442548X-RAY DIFFRACTION99.96
2.35-2.390.31791470.3052581X-RAY DIFFRACTION100
2.39-2.430.35651330.29752573X-RAY DIFFRACTION99.82
2.43-2.480.33511320.28392602X-RAY DIFFRACTION99.93
2.48-2.530.32641490.27682560X-RAY DIFFRACTION99.96
2.53-2.580.31831440.26032588X-RAY DIFFRACTION99.93
2.58-2.640.28331500.2532565X-RAY DIFFRACTION99.96
2.64-2.710.29771280.25272603X-RAY DIFFRACTION99.93
2.71-2.780.26631580.24242570X-RAY DIFFRACTION99.85
2.78-2.860.33211410.24062601X-RAY DIFFRACTION99.96
2.86-2.960.29411310.24752606X-RAY DIFFRACTION99.93
2.96-3.060.22861350.25322607X-RAY DIFFRACTION99.96
3.06-3.180.26171100.24592658X-RAY DIFFRACTION100
3.18-3.330.28881510.23622602X-RAY DIFFRACTION100
3.33-3.510.2621280.22492634X-RAY DIFFRACTION100
3.51-3.720.24011290.21052656X-RAY DIFFRACTION99.96
3.73-4.010.21181460.18912645X-RAY DIFFRACTION99.96
4.01-4.420.18921300.17632698X-RAY DIFFRACTION99.96
4.42-5.050.18161520.16612669X-RAY DIFFRACTION100
5.05-6.360.21821740.19882715X-RAY DIFFRACTION100
6.36-43.980.21071280.20162944X-RAY DIFFRACTION99.51
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)
12.86338282472-0.881015398944-0.04275530519014.381826936680.1439698389481.072804185220.02385805492610.401206671320.0177590954253-0.408187664309-0.438648760424-0.2800030518810.03855287779490.1771405176620.3925127812940.5607010501560.07519104419280.09576841702750.6723802579180.1863673566190.486660412885-27.255413824340.219603015216.6877963716
27.14453349447-6.44506534988-4.2669411635.781084178253.985316772952.601874997650.2928798057590.5967658276410.302709339627-0.7382519930950.0892521454138-0.7650003026640.207174867201-0.181409452375-0.6292474034020.933560696419-0.01658758274760.1932391075720.5729408835640.1102241191620.592400232926-7.7277042972344.15449672596.97567933942
32.384432353790.442335590078-0.1341702617432.023444391630.3125033396361.50490860337-0.257163287793-0.108074761205-0.65656190065-0.2915858457480.003848027465940.1458325600220.469180124019-0.04571669927380.2398497080870.6573810599860.06640606246010.1946155003320.6168779309380.2186696280170.648576733572-29.072094442222.179925119726.7587662019
42.245452434570.402389718988-1.707431077333.1758997204-0.7476504337713.30203412171-0.1689465340270.229261823807-0.403414971595-0.2243611392650.217140929054-0.1946430449440.212085526639-0.0935424816138-0.06913344290550.7861427611840.04325385834030.2508834503780.689972132130.1050658268690.681179361896-8.8390335685823.387381528710.3562193597
52.37632920887-0.8693741064930.9311037201884.57110424612-2.820250536915.08134950503-0.55270555060.2681114436540.5844174642050.616227430858-0.500686579672-0.852011269068-0.8432756849660.7096180670170.4097734929090.728489798938-0.115690638717-0.2878949094150.8522131835290.3694784234590.854180069164-17.843961288649.437230145235.9065407098
62.54830003121-2.158288092170.6645085271324.24524579697-0.402901150381.65871170924-0.02740240554990.3489636589840.62012816293-0.124440923352-0.69605491699-1.726647399340.02854948765520.9515819979370.2725471147270.4732082446830.03022920190820.0978959451151.281385592450.6664274859481.24051550847-3.4579662108533.911533617935.2665822108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 259 )
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 382 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 110 )
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 383 )

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