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- PDB-4ojt: Helicobacter pylori MTAN complexed with S-ribosylhomocysteine and... -

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Basic information

Entry
Database: PDB / ID: 4ojt
TitleHelicobacter pylori MTAN complexed with S-ribosylhomocysteine and adenine
ComponentsMTA/SAH 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
S-ribosylhomocysteine / ADENINE / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5093
Polymers25,1071
Non-polymers4022
Water3,963220
1
A: MTA/SAH nucleosidase
hetero molecules

A: MTA/SAH nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0196
Polymers50,2142
Non-polymers8054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area4200 Å2
ΔGint-22 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.241, 81.241, 67.456
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-405-

HOH

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Components

#1: Protein MTA/SAH nucleosidase / 5'-methylthioadenosine nucleosidase / S-adenosylhomocysteine nucleosidase


Mass: 25106.951 Da / Num. of mol.: 1 / Fragment: UNP residues 2-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: jhp_0082, mtn, mtnN, pfs / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase
#2: Sugar ChemComp-2WP / S-ribosylhomocysteine / (2S)-2-amino-4-({[(2S,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid


Type: D-saccharide, alpha linking / Mass: 267.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO6S
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, 30 % (v/v) PEG-MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2011
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 40628 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 46.389
Reflection shellResolution: 1.5→1.5402 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.798 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1979 4.87 %RANDOM
Rwork0.182 ---
obs0.1831 40628 98.37 %-
all-40628 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.346 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0537 Å2-0 Å2-0 Å2
2--3.0537 Å20 Å2
3----6.1073 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 27 220 2010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061821
X-RAY DIFFRACTIONf_angle_d0.9932452
X-RAY DIFFRACTIONf_dihedral_angle_d12.929654
X-RAY DIFFRACTIONf_chiral_restr0.069286
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54020.26771340.24482626X-RAY DIFFRACTION95
1.5402-1.58180.26251390.22662700X-RAY DIFFRACTION98
1.5818-1.62840.25191340.21192723X-RAY DIFFRACTION98
1.6284-1.68090.2171400.19862727X-RAY DIFFRACTION98
1.6809-1.7410.21931370.18612720X-RAY DIFFRACTION98
1.741-1.81070.21361400.19282751X-RAY DIFFRACTION98
1.8107-1.89310.22171420.18582758X-RAY DIFFRACTION99
1.8931-1.99290.21891420.18842746X-RAY DIFFRACTION98
1.9929-2.11770.21451410.18072757X-RAY DIFFRACTION99
2.1177-2.28120.19911380.18162785X-RAY DIFFRACTION99
2.2812-2.51070.2081450.18782802X-RAY DIFFRACTION99
2.5107-2.87390.2331480.18352806X-RAY DIFFRACTION100
2.8739-3.62020.19851480.18322845X-RAY DIFFRACTION100
3.6202-34.80760.1721510.16232903X-RAY DIFFRACTION98

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