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- PDB-6wkb: Human S-adenosylmethionine synthetase co-crystallized with UppNHp... -

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Basic information

Entry
Database: PDB / ID: 6wkb
TitleHuman S-adenosylmethionine synthetase co-crystallized with UppNHp and Met
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / S-adenosylmethionine synthetase
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
D-METHIONINE / METHIONINE / 5'-deoxyuridine / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTan, L.L. / Jackson, C.J.
CitationJournal: To Be Published
Title: S-adenosylmethionine synthetase
Authors: Laurino, P. / Jackson, C.J. / Tan, L.L.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

Downloads & links

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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)88,2587
Polymers87,4412
Non-polymers8175
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-25 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.191, 144.191, 188.196
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#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: pET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase

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Non-polymers , 5 types, 33 molecules

#2: Chemical ChemComp-U4P / 5'-deoxyuridine / Deoxyuridine


Mass: 228.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O5 / Comment: antivirus*YM
#3: Chemical ChemComp-MED / D-METHIONINE / Methionine


Type: D-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 3350, 0.1 M Bis-Tris pH 6.5, 10% ethylene glycol
PH range: 6.0 - 7.0

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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: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.55→47.2 Å / Num. obs: 38275 / % possible obs: 99.9 % / Redundancy: 39.1 % / Biso Wilson estimate: 75.41 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 2.55→2.66 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4574 / CC1/2: 0.645 / Χ2: 0.99 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A1I

5a1i


Resolution: 2.55→47.2 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1967 5.16 %
Rwork0.2202 --
obs0.2225 38107 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 54 28 5999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0016240
X-RAY DIFFRACTIONf_angle_d0.4758447
X-RAY DIFFRACTIONf_dihedral_angle_d15.7852297
X-RAY DIFFRACTIONf_chiral_restr0.043941
X-RAY DIFFRACTIONf_plane_restr0.0031094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.4311580.41132471X-RAY DIFFRACTION99
2.61-2.680.41661360.38072520X-RAY DIFFRACTION99
2.68-2.760.35721190.34912550X-RAY DIFFRACTION100
2.76-2.850.3921440.32622532X-RAY DIFFRACTION100
2.85-2.950.41821500.31832525X-RAY DIFFRACTION100
2.95-3.070.43721380.29922548X-RAY DIFFRACTION100
3.07-3.210.31521260.26632560X-RAY DIFFRACTION99
3.21-3.380.36651320.25962557X-RAY DIFFRACTION100
3.38-3.590.31161500.2392567X-RAY DIFFRACTION100
3.59-3.870.24651270.21412589X-RAY DIFFRACTION100
3.87-4.260.25361470.18932601X-RAY DIFFRACTION100
4.26-4.880.19971420.16572617X-RAY DIFFRACTION100
4.88-6.140.20541720.1922644X-RAY DIFFRACTION100
6.14-47.20.23651260.20332859X-RAY DIFFRACTION100
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)
12.95621.490.1241.9908-1.11162.7139-0.131-0.32910.1787-0.0023-0.1170.2352-0.36460.1050.08310.75510.06770.08140.6191-0.00840.52899.2597-39.315932.2277
24.32641.233-1.2191.6273-0.96922.7402-0.1207-0.55670.62140.0037-0.0657-0.1053-0.68890.26930.14490.9561-0.00680.02130.5811-0.01540.73939.9341-37.960729.5279
35.3837-0.9449-0.85331.7540.78414.3577-0.8241.0263-0.82730.02740.06390.2841.0015-0.83370.7811.2028-0.29310.23791.1278-0.09540.69197.0008-52.2329.7375
43.4662-0.8619-0.68592.61280.21593.3272-0.10090.15620.6330.01220.19-0.5287-0.71360.7061-0.1111.0581-0.21190.10120.810.01370.770924.9989-34.609124.5938
51.3801-0.67430.59380.95130.37931.46540.064-0.0488-0.03390.08650.0008-0.0436-0.1203-0.1202-0.02120.5922-0.20570.11760.85940.14030.630415.2243-56.882645.4525
63.3994-3.4836-5.06883.56534.85698.88950.23921.3441-0.6296-0.2547-1.17581.70810.0039-2.89030.74830.945-0.0034-0.06651.4864-0.11340.77018.0581-65.973326.0571
71.688-0.0645-0.45342.0617-0.02473.0156-0.09630.35490.1182-0.27950.2317-0.153-0.20710.531-0.19960.6077-0.28610.11550.93930.08630.742931.6805-55.617134.6832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 395 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 104 )
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 138 )
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 395 )

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