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

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Basic information

Entry
Database: PDB / ID: 6rka
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 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / S-ADENOSYLMETHIONINE / :
Function and homology information
Biological speciesUreaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,52410
Polymers171,5224
Non-polymers2,0016
Water1086
1
A: Methionine adenosyltransferase
B: Methionine adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1745
Polymers85,7612
Non-polymers1,4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-20 kcal/mol
Surface area26300 Å2
MethodPISA
2
C: Methionine adenosyltransferase
D: Methionine adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3505
Polymers85,7612
Non-polymers5883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-34 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.468, 114.468, 228.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2m Li2SO4, 0.1M Tris pH 8.5 and 25% PEG 3350

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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 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→46.62 Å / Num. obs: 50487 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.309 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 0.61 / Num. unique obs: 4625 / CC1/2: 0.397

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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: 2.5→46.62 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.272 --
Rwork0.233 --
obs-47786 99.77 %
Refinement stepCycle: LAST / Resolution: 2.5→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11544 0 126 6 11676

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