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- PDB-6k2q: Aeromonas hydrophila MtaN-2 complexed with adenine -

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Basic information

Entry
Database: PDB / ID: 6k2q
TitleAeromonas hydrophila MtaN-2 complexed with adenine
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / Aeromonas hydrophila / MtaN-2 / Complex / Adenine / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Function / homology
Function and homology information


L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / cytosol
Similarity search - Function
MTA/SAH nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological specieseromonas hydrophila subsp. hydrophila ATCC 7966 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, J. / Liu, W. / Wang, L. / Shang, F. / Lan, J. / Chen, Y. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: Biochemistry / Year: 2019
Title: Crystal Structure of Aeromonas hydrophila Cytoplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase.
Authors: Chen, J. / Liu, W. / Wang, L. / Shang, F. / Chen, Y. / Lan, J. / Gao, P. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y.
History
DepositionMay 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5428
Polymers113,0024
Non-polymers5414
Water12,250680
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7714
Polymers56,5012
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-27 kcal/mol
Surface area17700 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7714
Polymers56,5012
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-27 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.939, 74.939, 185.214
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase / SRH nucleosidase


Mass: 28250.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) eromonas hydrophila subsp. hydrophila ATCC 7966 (bacteria)
Gene: mtnN, mtnN-2, AHA_1706 / Plasmid: pPROEX-HTA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)
References: UniProt: A0KIZ1, adenosylhomocysteine nucleosidase
#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M Magnesium sulfate, 0.1M TRIS hydrochloride, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 76730 / % possible obs: 97.68 % / Redundancy: 4 % / Rsym value: 0.185 / Net I/σ(I): 25.64
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.19 / Num. unique obs: 3820 / Rpim(I) all: 0.287 / % possible all: 93.95

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WKB

4wkb


Resolution: 2→32.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.61
RfactorNum. reflection% reflection
Rfree0.1946 2001 2.61 %
Rwork0.1605 --
obs0.1614 76715 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6748 0 40 680 7468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136892
X-RAY DIFFRACTIONf_angle_d1.1659286
X-RAY DIFFRACTIONf_dihedral_angle_d6.5584146
X-RAY DIFFRACTIONf_chiral_restr0.0611064
X-RAY DIFFRACTIONf_plane_restr0.0071206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.27081270.24585011X-RAY DIFFRACTION93
2.0502-2.10570.24361430.22565346X-RAY DIFFRACTION97
2.1057-2.16760.27421410.21435307X-RAY DIFFRACTION97
2.1676-2.23750.23391410.19695368X-RAY DIFFRACTION98
2.2375-2.31750.26411460.1895355X-RAY DIFFRACTION98
2.3175-2.41030.20831380.16865378X-RAY DIFFRACTION98
2.4103-2.51990.22991500.1685165X-RAY DIFFRACTION95
2.5199-2.65270.2061430.16245427X-RAY DIFFRACTION99
2.6527-2.81880.21171500.15645431X-RAY DIFFRACTION100
2.8188-3.03630.18231440.15525439X-RAY DIFFRACTION100
3.0363-3.34160.21181440.15465450X-RAY DIFFRACTION100
3.3416-3.82450.15961470.14665345X-RAY DIFFRACTION98
3.8245-4.81590.16791460.12915257X-RAY DIFFRACTION96
4.8159-32.45380.17971410.1645435X-RAY DIFFRACTION99

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