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- PDB-4l4q: Methionine Adenosyltransferase -

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Basic information

Entry
Database: PDB / ID: 4l4q
TitleMethionine Adenosyltransferase
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / cytoplasmic
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
S-adenosylmethionine synthetase, domain 2 / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSchlesier, J. / Siegrist, J. / Gerhardt, S. / Andexer, J.N. / Einsle, O.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: Structural and functional characterisation of the methionine adenosyltransferase from Thermococcus kodakarensis.
Authors: Schlesier, J. / Siegrist, J. / Gerhardt, S. / Erb, A. / Blaesi, S. / Richter, M. / Einsle, O. / Andexer, J.N.
History
DepositionJun 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase


Theoretical massNumber of molelcules
Total (without water)178,6924
Polymers178,6924
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15500 Å2
ΔGint-29 kcal/mol
Surface area56930 Å2
MethodPISA
2
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase


Theoretical massNumber of molelcules
Total (without water)89,3462
Polymers89,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-11 kcal/mol
Surface area31060 Å2
MethodPISA
3
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase


Theoretical massNumber of molelcules
Total (without water)89,3462
Polymers89,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-10 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.839, 57.792, 236.434
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44672.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: mat, metK, TK0545 / Plasmid: pET28+::metK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CodonPlus-RP / References: UniProt: Q5JF22, methionine adenosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES/NaOH pH 7.5, 35% pentaerythritol, propoxylate, 3% (w/v) sucrose, 0.2 M potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 120317 / Num. obs: 119397 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.69 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.1012 / Net I/σ(I): 9.17

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Processing

Software
NameVersionClassification
ALBULAdata collection
SHARPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→46.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.236 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24463 5999 5 %RANDOM
Rwork0.18685 ---
all0.18966 120317 --
obs0.18966 113983 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.991 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20.18 Å2
2--2.59 Å2-0 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12487 0 0 654 13141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912744
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212515
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.97317271
X-RAY DIFFRACTIONr_angle_other_deg0.968328871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9351615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50524.973565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.588152287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.861572
X-RAY DIFFRACTIONr_chiral_restr0.1420.21977
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022637
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 444 -
Rwork0.295 8362 -
obs--99.94 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.11670.1092-0.19890.1608-0.02521.02830.08250.0219-0.05620.0251-0.0477-0.1172-0.3486-0.2007-0.03490.13990.0884-0.01630.10440.04720.133323.875711.517134.1008
20.2280.0607-0.14540.1146-0.01290.9637-0.05360.0431-0.0419-0.0205-0.0756-0.10950.2473-0.35250.12920.0959-0.0520.01590.21490.00240.160919.3405-11.683729.0706
30.1647-0.0485-0.19080.08130.05310.99880.06930.124400.0664-0.1071-0.0564-0.3662-0.35460.03780.24720.0341-0.08140.23640.03920.05696.19385.180182.3503
40.1958-0.0255-0.28830.08210.03371.1017-0.09070.0770.00630.0908-0.0687-0.08040.2995-0.18750.15940.1687-0.1281-0.0350.12640.02390.12912.2981-18.082879.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 405
2X-RAY DIFFRACTION2B5 - 405
3X-RAY DIFFRACTION3C4 - 405
4X-RAY DIFFRACTION4D4 - 405

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