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- PDB-6rk5: Inter-dimeric interface controls function and stability of S-meth... -

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Basic information

Entry
Database: PDB / ID: 6rk5
TitleInter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum
ComponentsMethionine adenosyltransferase
KeywordsTRANSFERASE / synthetase
Function / homologyGMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesUreaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShahar, A. / Zarivach, R. / Bershtein, S. / Kleiner, D. / Shmulevich, F.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1630/15 Israel
CitationJournal: J.Mol.Biol. / Year: 2019
Title: The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase.
Authors: Kleiner, D. / Shmulevich, F. / Zarivach, R. / Shahar, A. / Sharon, M. / Ben-Nissan, G. / Bershtein, S.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Methionine adenosyltransferase
B: Methionine adenosyltransferase
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)171,5224
Polymers171,5224
Non-polymers00
Water3,045169
1
A: Methionine adenosyltransferase
B: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)85,7612
Polymers85,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-21 kcal/mol
Surface area27200 Å2
MethodPISA
2
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)85,7612
Polymers85,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-21 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.358, 80.450, 158.849
Angle α, β, γ (deg.)90.00, 94.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methionine adenosyltransferase


Mass: 42880.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)
Gene: metK, UUR7_0462 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: B2NE58, methionine adenosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1M Hepes pH 7.4 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→47.6 Å / Num. obs: 42328 / % possible obs: 96.8 % / Redundancy: 7.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.394 / Num. unique obs: 13239 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RJS

6rjs


Resolution: 2.6→47.6 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.209 --
obs-42309 95.54 %
Refinement stepCycle: LAST / Resolution: 2.6→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 0 169 11549

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