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- PDB-4p54: Crystal Structure of the Helicobacter pylori MTAN-D198N mutant wi... -

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Basic information

Entry
Database: PDB / ID: 4p54
TitleCrystal Structure of the Helicobacter pylori MTAN-D198N mutant with 5'-methylthioadenosine in the active site.
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHYDROLASE / homodimer
Function / homology
Function and homology information


aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / 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
5'-DEOXY-5'-METHYLTHIOADENOSINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRonning, D.R. / Mishra, V.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite.
Authors: Mishra, V. / Ronning, D.R.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4393
Polymers25,1061
Non-polymers3332
Water6,179343
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8786
Polymers50,2122
Non-polymers6664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Buried area4870 Å2
ΔGint-46 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.207, 81.207, 67.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-711-

HOH

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Components

#1: Protein Aminodeoxyfutalosine nucleosidase / Aminofutalosine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / ...Aminofutalosine nucleosidase / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 6-amino-6-deoxyfutalosine N-ribosylhydrolase


Mass: 25105.965 Da / Num. of mol.: 1 / Mutation: D198N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride, 0.1 M HEPES pH 7.5 and 25 % (w/v) PEG-3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.63→24.73 Å / Num. obs: 32308 / % possible obs: 99.7 % / Redundancy: 10.8 % / Net I/σ(I): 11.7
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.3 / % possible all: 99.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NM6

3nm6


Resolution: 1.65→24.73 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1518 4.94 %Random selection
Rwork0.1586 ---
obs0.1597 30701 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.019 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5266 Å2-0 Å2-0 Å2
2--1.5266 Å20 Å2
3----3.0531 Å2
Refinement stepCycle: LAST / Resolution: 1.65→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 21 343 2127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061815
X-RAY DIFFRACTIONf_angle_d0.9632414
X-RAY DIFFRACTIONf_dihedral_angle_d16.242649
X-RAY DIFFRACTIONf_chiral_restr0.065281
X-RAY DIFFRACTIONf_plane_restr0.004308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.17341430.14532759X-RAY DIFFRACTION95
1.709-1.77740.1911380.15532818X-RAY DIFFRACTION96
1.7774-1.85820.17571410.16322841X-RAY DIFFRACTION97
1.8582-1.95620.19661900.16382842X-RAY DIFFRACTION97
1.9562-2.07870.17041590.15432919X-RAY DIFFRACTION99
2.0787-2.23910.17591400.15082957X-RAY DIFFRACTION99
2.2391-2.46420.16971260.16162972X-RAY DIFFRACTION100
2.4642-2.82040.17991670.16742961X-RAY DIFFRACTION100
2.8204-3.55170.17691460.15933010X-RAY DIFFRACTION100
3.5517-24.73240.17481680.15213104X-RAY DIFFRACTION99

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