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

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Basic information

Entry
Database: PDB / ID: 6rjs
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 29, 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
C: Methionine adenosyltransferase
B: Methionine adenosyltransferase
D: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)168,7604
Polymers168,7604
Non-polymers00
Water1,49583
1
A: Methionine adenosyltransferase
B: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)84,3802
Polymers84,3802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-19 kcal/mol
Surface area26820 Å2
MethodPISA
2
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase


Theoretical massNumber of molelcules
Total (without water)84,3802
Polymers84,3802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-16 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.205, 64.064, 114.495
Angle α, β, γ (deg.)77.93, 83.86, 73.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Methionine adenosyltransferase


Mass: 42189.879 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.: 83 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5% Tacsimate, 0.1M Hepes pH 7.0, 10% PEG 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→111.81 Å / Num. obs: 42461 / % possible obs: 92.02 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.055 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.73 Å / Rmerge(I) obs: 0.648 / Num. unique obs: 12471 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T8S

5t8s


Resolution: 2.6→47.62 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.246 --
Rwork0.212 --
obs-40410 92.08 %
Refinement stepCycle: LAST / Resolution: 2.6→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11313 0 0 83 11396

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