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- PDB-1xrb: S-adenosylmethionine synthetase (MAT, ATP: L-methionine S-adenosy... -

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Basic information

Entry
Database: PDB / ID: 1xrb
TitleS-adenosylmethionine synthetase (MAT, ATP: L-methionine S-adenosyltransferase, E.C.2.5.1.6) in which MET residues are replaced with selenomethionine residues (MSE)
ComponentsS-ADENOSYLMETHIONINE SYNTHETASE
KeywordsTRANSFERASE / METHYLTRANSFERASE
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / S-adenosylmethionine cycle / potassium ion binding / one-carbon metabolic process / magnesium ion binding / ATP binding / identical protein binding / cytosol
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 / S-adenosylmethionine synthase / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsTakusagawa, F. / Kamitori, S. / Misaki, S. / Markham, G.D.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: Crystal structure of S-adenosylmethionine synthetase.
Authors: Takusagawa, F. / Kamitori, S. / Misaki, S. / Markham, G.D.
History
DepositionOct 26, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6067
Polymers42,2891
Non-polymers3176
Water00
1
A: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules

A: S-ADENOSYLMETHIONINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,21214
Polymers84,5792
Non-polymers63312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)128.900, 128.900, 139.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Atom site foot note1: GLY 13 - HIS 14 OMEGA = 147.84 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ASP 173 - ASP 174 OMEGA = 215.56 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ASP 194 - GLN 195 OMEGA = 212.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY 228 - ARG 229 OMEGA = 238.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: GLY 259 - GLY 260 OMEGA = 227.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-414-

K

DetailsTHE TETRAMERIC ENZYME CAN BE GENERATED BY THE FOLLOWING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS: X, Y, Z, -X, Y-X, 1/3-Z -X, 1-Y, Z X, 1+X-Y, 1/3-Z

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Components

#1: Protein S-ADENOSYLMETHIONINE SYNTHETASE / MAT / ATP:L-METHIONINE S-ADENOSYLTRANSFERASE


Mass: 42289.363 Da / Num. of mol.: 1 / Mutation: MET RESIDUES ARE REPLACED WITH SELENOMETHIONINE / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P04384, UniProt: P0A817*PLUS, methionine adenosyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal grow
*PLUS
Temperature: 26 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMpotassium phosphate11
210 mM11MgCl2
333 %(v/v)ammonium sulfate11
410 mg/mlprotein11

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 62929 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 13507 / % possible obs: 97.7 % / Num. measured all: 62929 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→10 Å / σ(I): 2.77
RfactorNum. reflection% reflection
Rfree0.265 --
Rwork0.188 --
obs0.188 13507 97.7 %
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3534 0 14 0 3548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 25.8
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.13 Å / Total num. of bins used: 8 / Num. reflection obs: 1604 / Rfactor obs: 0.279

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