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- PDB-6dyv: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S... -

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Basic information

Entry
Database: PDB / ID: 6dyv
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-((pent-4-yn-1-ylthio)methyl)pyrrolidin-3-ol
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MTAN enzyme / duodenal ulcers / stomach cancer / HYDROLASE-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-OS3 / adenosylhomocysteine nucleosidase / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Selective Inhibitors of Helicobacter pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase.
Authors: Harijan, R.K. / Hoff, O. / Ducati, R.G. / Firestone, R.S. / Hirsch, B.M. / Evans, G.B. / Schramm, V.L. / Tyler, P.C.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,02313
Polymers53,7742
Non-polymers1,25011
Water8,593477
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,08514
Polymers53,7742
Non-polymers1,31212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4820 Å2
ΔGint-13 kcal/mol
Surface area17470 Å2
MethodPISA
2
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,96112
Polymers53,7742
Non-polymers1,18710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444-y-1,-x-1,-z-1/21
Buried area4520 Å2
ΔGint-17 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.479, 73.479, 176.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: -1 - 230 / Label seq-ID: 14 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 26886.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BW246_00770, BZL55_04980, CEP79_03920 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1W0VQJ9, UniProt: Q9ZMY2*PLUS, adenosylhomocysteine nucleosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-OS3 / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(pent-4-yn-1-yl)sulfanyl]methyl}pyrrolidin-3-ol


Mass: 345.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N5OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.2 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, pH 7.5, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2017 / Details: KB mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.62→88.1 Å / Num. obs: 61452 / % possible obs: 98.7 % / Redundancy: 13.9 % / CC1/2: 0.998 / Net I/σ(I): 14.8
Reflection shellResolution: 1.62→1.65 Å / Num. measured obs: 25016 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4WKP

4wkp


Resolution: 1.62→67.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.704 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 3055 5 %RANDOM
Rwork0.16672 ---
obs0.16803 58317 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.62→67.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 84 481 4090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193734
X-RAY DIFFRACTIONr_bond_other_d0.0020.023562
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9815028
X-RAY DIFFRACTIONr_angle_other_deg0.95538285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81625.646147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03615657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.931156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1731.8921894
X-RAY DIFFRACTIONr_mcbond_other1.1721.8911893
X-RAY DIFFRACTIONr_mcangle_it1.8112.8322378
X-RAY DIFFRACTIONr_mcangle_other1.8112.8332379
X-RAY DIFFRACTIONr_scbond_it1.9152.1771838
X-RAY DIFFRACTIONr_scbond_other1.9152.1771839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.983.1552651
X-RAY DIFFRACTIONr_long_range_B_refined4.78524.5614278
X-RAY DIFFRACTIONr_long_range_B_other4.78424.5624279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14720 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 180 -
Rwork0.264 3707 -
obs--85.73 %

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