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- PDB-6if8: Aeromonas hydrophila MtaN-2 complexed with adenine -

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Basic information

Entry
Database: PDB / ID: 6if8
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
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 speciesAeromonas hydrophila subsp. hydrophila (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: To Be Published
Title: Aeromonas hydrophila MtaN-2 complexed with adenine
Authors: Chen, J. / Liu, W. / Wang, L. / Shang, F. / Lan, J. / Chen, Y. / Xu, Y.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

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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 area3100 Å2
ΔGint-28 kcal/mol
Surface area17570 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 area3140 Å2
ΔGint-27 kcal/mol
Surface area17740 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.) Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240) (bacteria)
Strain: ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240
Gene: mtnN, mtnN-2, AHA_1706 / Plasmid: pPROEX-HTA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0KIZ1, adenosylhomocysteine nucleosidase
#2: Chemical
ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water / 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
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: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.08
RfactorNum. reflection% reflection
Rfree0.1905 2001 2.61 %
Rwork0.153 --
obs0.154 76717 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_d0.0136915
X-RAY DIFFRACTIONf_angle_d1.49316
X-RAY DIFFRACTIONf_dihedral_angle_d15.6442506
X-RAY DIFFRACTIONf_chiral_restr0.061070
X-RAY DIFFRACTIONf_plane_restr0.0061208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.28151270.24955011X-RAY DIFFRACTION93
2.0502-2.10570.25591430.235346X-RAY DIFFRACTION97
2.1057-2.16760.27821410.21055307X-RAY DIFFRACTION97
2.1676-2.23750.2361410.19095368X-RAY DIFFRACTION98
2.2375-2.31750.24921460.1795355X-RAY DIFFRACTION98
2.3175-2.41030.20081380.16145377X-RAY DIFFRACTION98
2.4103-2.51990.21761500.1645165X-RAY DIFFRACTION95
2.5199-2.65270.19811430.1565427X-RAY DIFFRACTION99
2.6527-2.81880.20281500.15215431X-RAY DIFFRACTION100
2.8188-3.03630.17951440.1495439X-RAY DIFFRACTION100
3.0363-3.34160.21241440.15025450X-RAY DIFFRACTION100
3.3416-3.82450.14731470.145345X-RAY DIFFRACTION98
3.8245-4.81590.16781460.12115257X-RAY DIFFRACTION96
4.8159-32.45380.17571410.14925438X-RAY DIFFRACTION99

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