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- PDB-5h9u: Crystal structure of a thermostable methionine adenosyltransferase -

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Basic information

Entry
Database: PDB / ID: 5h9u
TitleCrystal structure of a thermostable methionine adenosyltransferase
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / tetramer / complex / methionine adenosyltransferase
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
S-adenosylmethionine synthase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.667 Å
AuthorsFeng, Y. / Wang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400635 China
Beijing Natural Science Foundation5154031 China
CitationJournal: To Be Published
Title: Crystal structure of a thermostable methionine adenosyltransferase
Authors: Feng, Y. / Wang, W.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 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
C: S-adenosylmethionine synthase
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase


Theoretical massNumber of molelcules
Total (without water)180,7894
Polymers180,7894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-51 kcal/mol
Surface area53950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.024, 77.053, 96.792
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45197.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: metK, TT_C1279 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72I53, methionine adenosyltransferase

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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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.01M Iron chloride hexahydrate, 0.1M Sodium citrate tribasic dehydrate pH 5.6, 10% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.667→43.2397 Å / Num. obs: 44867 / % possible obs: 100 % / Redundancy: 5.1 % / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
HKL-2000data collection
RefinementResolution: 2.667→43.2397 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 2264 5.05 %
Rwork0.1729 --
obs0.1759 44810 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.667→43.2397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12140 0 0 0 12140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612380
X-RAY DIFFRACTIONf_angle_d1.25616832
X-RAY DIFFRACTIONf_dihedral_angle_d15.154644
X-RAY DIFFRACTIONf_chiral_restr0.0521932
X-RAY DIFFRACTIONf_plane_restr0.0072196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6671-2.72510.29041200.21542496X-RAY DIFFRACTION95
2.7251-2.78850.29041370.20462640X-RAY DIFFRACTION100
2.7885-2.85820.27441460.20352690X-RAY DIFFRACTION100
2.8582-2.93540.28211360.20512624X-RAY DIFFRACTION100
2.9354-3.02180.30061270.20862711X-RAY DIFFRACTION100
3.0218-3.11930.28521480.21962617X-RAY DIFFRACTION100
3.1193-3.23070.25941690.18732624X-RAY DIFFRACTION100
3.2307-3.36010.24631410.17592663X-RAY DIFFRACTION100
3.3601-3.51290.2251320.17262660X-RAY DIFFRACTION100
3.5129-3.6980.27241420.17152672X-RAY DIFFRACTION100
3.698-3.92960.23581230.16482676X-RAY DIFFRACTION100
3.9296-4.23270.21381430.15592668X-RAY DIFFRACTION100
4.2327-4.65830.20331470.14642680X-RAY DIFFRACTION100
4.6583-5.33130.18131620.14512670X-RAY DIFFRACTION100
5.3313-6.71280.24021470.18532693X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 450.7248 Å / Origin y: -42.6442 Å / Origin z: 104.0213 Å
111213212223313233
T0.1205 Å20.0411 Å2-0.0157 Å2-0.0579 Å2-0.0451 Å2--0.0848 Å2
L0.345 °20.0403 °20.0022 °2-0.6065 °2-0.3664 °2--0.4241 °2
S0.0092 Å °0.011 Å °0.0134 Å °-0.0461 Å °0.0633 Å °0.1533 Å °-0.009 Å °-0.0921 Å °0.0185 Å °
Refinement TLS groupSelection details: all

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