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- PDB-4ynb: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S... -

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Basic information

Entry
Database: PDB / ID: 4ynb
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with pyrazinylthio-DADMe-Immucillin-A
ComponentsAminodeoxyfutalosine nucleosidase
KeywordsHydrolase/inhibitor / Hydrolase-inhibitor complex
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
Chem-4EH / DI(HYDROXYETHYL)ETHER / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCameron, S.A. / Wang, S. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM041916 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2015
Title: New Antibiotic Candidates against Helicobacter pylori.
Authors: Wang, S. / Cameron, S.A. / Clinch, K. / Evans, G.B. / Wu, Z. / Schramm, V.L. / Tyler, P.C.
#1: Journal: Biochemistry / Year: 2012
Title: A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori.
Authors: Wang, S. / Haapalainen, A.M. / Yan, F. / Du, Q. / Tyler, P.C. / Evans, G.B. / Rinaldo-Matthis, A. / Brown, R.L. / Norris, G.E. / Almo, S.C. / Schramm, V.L.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5355
Polymers26,8871
Non-polymers6484
Water3,495194
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,06910
Polymers53,7742
Non-polymers1,2958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_555-x,-z,-y1
Buried area4760 Å2
ΔGint-22 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.512, 157.512, 157.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-304-

PEG

21A-433-

HOH

31A-460-

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: 26886.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: mtnN, mtn, jhp_0082 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZMY2, aminodeoxyfutalosine nucleosidase, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-4EH / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol


Mass: 357.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N7OS
#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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.03 Å3/Da / Density % sol: 59.38 % / Description: Cubes
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mg/mL); Reservoir (0.2 M di-sodium phosphate and 2.2 M ammonium sulfate); Cryoprotection (20% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26571 / % possible obs: 100 % / Redundancy: 31.7 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.427 / Net I/av σ(I): 35.68 / Net I/σ(I): 6.6 / Num. measured all: 841660
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9323.10.71912811.471100
1.93-1.9728.213170.97100
1.97-2.0131.10.85812980.976100
2.01-2.0531.20.66613101.014100
2.05-2.0931.20.59713101.042100
2.09-2.1431.10.53113101.082100
2.14-2.1931.20.44413021.126100
2.19-2.2530.20.51113232.272100
2.25-2.3230.60.50413061.916100
2.32-2.3931.70.31913111.213100
2.39-2.48320.27313211.249100
2.48-2.5832.50.23513021.272100
2.58-2.733.10.18813231.37100
2.7-2.8433.80.16113391.47100
2.84-3.0234.40.13913241.513100
3.02-3.2534.80.10913291.777100
3.25-3.5834.60.09713581.929100
3.58-4.0932.90.09313501.848100
4.09-5.1632.70.07313771.413100
5.16-5032.30.06614801.45899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FFS

4ffs


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1772 / WRfactor Rwork: 0.158 / FOM work R set: 0.8435 / SU B: 3.135 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1386 / SU Rfree: 0.1221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.122 / SU Rfree Cruickshank DPI: 0.1221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 1076 4.8 %RANDOM
Rwork0.1753 ---
obs0.1763 21421 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.65 Å2 / Biso mean: 24.827 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 44 194 1991
Biso mean--35.06 32.4 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191847
X-RAY DIFFRACTIONr_bond_other_d0.0010.021803
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9842489
X-RAY DIFFRACTIONr_angle_other_deg0.7834169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73725.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851153
X-RAY DIFFRACTIONr_chiral_restr0.080.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_mcbond_it1.3122.217925
X-RAY DIFFRACTIONr_mcbond_other1.2852.214924
X-RAY DIFFRACTIONr_mcangle_it1.9483.3161156
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 70 -
Rwork0.185 1557 -
all-1627 -
obs--100 %

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