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- PDB-4oy3: Crystal Structure of the Helicobacter pylori MTAN-D198N mutant wi... -

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Basic information

Entry
Database: PDB / ID: 4oy3
TitleCrystal Structure of the Helicobacter pylori MTAN-D198N mutant with S-Adenosylhomocysteine 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 / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process
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
S-ADENOSYL-L-HOMOCYSTEINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMishra, V. / Ronning, D.R.
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
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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)25,5263
Polymers25,1061
Non-polymers4202
Water7,494416
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0526
Polymers50,2122
Non-polymers8404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area3800 Å2
ΔGint-51 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.733, 80.733, 67.199
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-629-

HOH

21A-736-

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 / Fragment: UNP residues 2-230 / 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, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5 and 30 % (v/v) PEG-MME 550.

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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 / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 75266 / % possible obs: 95 % / Redundancy: 10.9 % / Net I/σ(I): 16
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 4.1 / % possible all: 92.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1839) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→22.019 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1451 2003 2.66 %Random
Rwork0.1295 ---
obs0.1299 75260 95.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→22.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 27 416 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111897
X-RAY DIFFRACTIONf_angle_d1.392577
X-RAY DIFFRACTIONf_dihedral_angle_d16.116716
X-RAY DIFFRACTIONf_chiral_restr0.06303
X-RAY DIFFRACTIONf_plane_restr0.007327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.23010.13611360.11065044X-RAY DIFFRACTION92
1.2301-1.26340.13061360.10955088X-RAY DIFFRACTION93
1.2634-1.30050.181350.11075064X-RAY DIFFRACTION93
1.3005-1.34250.14211420.115126X-RAY DIFFRACTION94
1.3425-1.39050.15791410.11375143X-RAY DIFFRACTION94
1.3905-1.44610.13771440.10815163X-RAY DIFFRACTION95
1.4461-1.51190.13081440.10155205X-RAY DIFFRACTION95
1.5119-1.59160.1351420.10365273X-RAY DIFFRACTION96
1.5916-1.69130.14071440.10815271X-RAY DIFFRACTION96
1.6913-1.82190.13321460.12355344X-RAY DIFFRACTION97
1.8219-2.00510.14281470.12665366X-RAY DIFFRACTION98
2.0051-2.2950.12911490.12445426X-RAY DIFFRACTION98
2.295-2.89040.14761510.14365509X-RAY DIFFRACTION99
2.8904-22.02270.16061460.1525235X-RAY DIFFRACTION91

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