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- PDB-5b7g: Structures and functional analysis of periplasmic 5-methylthioade... -

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Basic information

Entry
Database: PDB / ID: 5b7g
TitleStructures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila
ComponentsMTA/SAH nucleosidase
KeywordsHYDROLASE / Aeromonas hydrophila / MtaN-1 / MtaN-2 / SAH / MTA / 5-DAO
Function / homology
Function and homology information


methylthioadenosine nucleosidase / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside metabolic process / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / MTA/SAH nucleosidase
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsXu, Y.
Funding support China, 5items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31200556 China
the National Natural Science Foundation of China21272031 China
the National Natural Science Foundation of China21172028 China
the Program for Liaoning Excellent Talents in UniversityLJQ2015030 China
the Fundamental Research Funds for the Central UniversitiesDC201502020203 China
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila.
Authors: Xu, Y. / Wang, L. / Chen, J. / Zhao, J. / Fan, S. / Dong, Y. / Ha, N.C. / Quan, C.
History
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: 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 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: MTA/SAH nucleosidase
B: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9266
Polymers54,4712
Non-polymers4544
Water14,106783
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-16 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.671, 102.671, 118.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein MTA/SAH nucleosidase


Mass: 27235.615 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: ATCC 7966 / DSM 30187 / Gene: mtnN-1, AHA_0953 / Production host: Escherichia coli (E. coli)
References: UniProt: A0KGU9, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 4.6
Details: 6% (w/v) polyethylene glycol 4000, 0.1 M sodium acetate trihydrate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→49.49 Å / Num. obs: 142443 / % possible obs: 99.2 % / Redundancy: 6.5 % / Net I/σ(I): 14.79

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NM4

3nm4


Resolution: 1.399→29.639 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 7080 4.97 %
Rwork0.1487 --
obs0.1494 142443 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→29.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 32 783 4644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063986
X-RAY DIFFRACTIONf_angle_d1.0885426
X-RAY DIFFRACTIONf_dihedral_angle_d13.0421418
X-RAY DIFFRACTIONf_chiral_restr0.042597
X-RAY DIFFRACTIONf_plane_restr0.005708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3991-1.4150.23342240.19944459X-RAY DIFFRACTION100
1.415-1.43160.22072340.19284448X-RAY DIFFRACTION100
1.4316-1.44910.20372600.18124424X-RAY DIFFRACTION100
1.4491-1.46740.19482500.16914536X-RAY DIFFRACTION100
1.4674-1.48670.15592240.16564432X-RAY DIFFRACTION100
1.4867-1.50710.18492250.16184519X-RAY DIFFRACTION100
1.5071-1.52860.16642220.15364470X-RAY DIFFRACTION100
1.5286-1.55140.16812410.15224454X-RAY DIFFRACTION100
1.5514-1.57570.17042540.15234461X-RAY DIFFRACTION100
1.5757-1.60150.15052160.14834521X-RAY DIFFRACTION100
1.6015-1.62910.14842310.14334470X-RAY DIFFRACTION100
1.6291-1.65870.15432640.14744466X-RAY DIFFRACTION100
1.6587-1.69060.17042650.14834434X-RAY DIFFRACTION100
1.6906-1.72510.15792340.14444516X-RAY DIFFRACTION100
1.7251-1.76260.16082400.1484475X-RAY DIFFRACTION100
1.7626-1.80360.17632230.15184508X-RAY DIFFRACTION100
1.8036-1.84870.16332490.15424455X-RAY DIFFRACTION100
1.8487-1.89870.15962120.14974545X-RAY DIFFRACTION100
1.8987-1.95460.14382410.14534488X-RAY DIFFRACTION100
1.9546-2.01770.17412060.14614555X-RAY DIFFRACTION100
2.0177-2.08970.16232680.15274488X-RAY DIFFRACTION100
2.0897-2.17340.15892570.14764469X-RAY DIFFRACTION100
2.1734-2.27230.16092520.14214520X-RAY DIFFRACTION100
2.2723-2.3920.16912040.14764551X-RAY DIFFRACTION100
2.392-2.54180.15472110.15974574X-RAY DIFFRACTION100
2.5418-2.73790.16492170.14924544X-RAY DIFFRACTION100
2.7379-3.01320.16122520.14954582X-RAY DIFFRACTION100
3.0132-3.44870.162380.14064570X-RAY DIFFRACTION100
3.4487-4.34280.16152260.12994622X-RAY DIFFRACTION100
4.3428-29.64520.15412400.14784807X-RAY DIFFRACTION100

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