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

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Basic information

Entry
Database: PDB / ID: 4wko
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hydroxybutylthio-DADMe-Immucillin-A
ComponentsAminodeoxyfutalosine nucleosidase
Keywordshydrolase/hydrolase inhibitor / hydrolase / 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 / 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
Chem-GMD / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 20, 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 2.0Jun 6, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2382
Polymers26,8871
Non-polymers3511
Water3,999222
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4774
Polymers53,7742
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_555y,x,-z1
Buried area3500 Å2
ΔGint-31 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.256, 157.256, 157.256
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-422-

HOH

21A-469-

HOH

31A-471-

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, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-GMD / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol / hydroxybutylthio-DADMe-Immucillin-A


Mass: 351.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.01 Å3/Da / Density % sol: 59.18 % / Description: Cube
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: Jun 5, 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: 26379 / % possible obs: 100 % / Redundancy: 43.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.017 / Rrim(I) all: 0.114 / Χ2: 0.978 / Net I/av σ(I): 47.2 / Net I/σ(I): 7.3 / Num. measured all: 1157099
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9341.90.8765.8612860.9660.1360.8860.798100
1.93-1.9741.90.69913040.9740.1090.7080.796100
1.97-2.0142.30.56913080.9820.0880.5760.824100
2.01-2.0542.50.45612700.9880.070.4620.843100
2.05-2.0942.70.43413030.9880.0670.4390.843100
2.09-2.1442.70.37512930.9940.0580.380.856100
2.14-2.1942.90.31312940.9950.0480.3160.867100
2.19-2.2543.30.28213080.9960.0430.2850.888100
2.25-2.32430.2513040.9970.0380.2530.88100
2.32-2.3943.30.23112970.9970.0350.2340.891100
2.39-2.4843.50.20213130.9980.0310.2040.882100
2.48-2.5843.80.17713100.9990.0270.1790.903100
2.58-2.744.20.14613000.9990.0220.1480.938100
2.7-2.8444.60.12913290.9990.0190.1311.005100
2.84-3.0245.80.11613180.9990.0170.1171.136100
3.02-3.2546.60.09113180.9990.0130.0921.333100
3.25-3.5846.40.067135410.010.0681.198100
3.58-4.09450.047133810.0070.0481.254100
4.09-5.16460.038136210.0060.0381.241100
5.16-5044.40.035147010.0050.0351.03799.9

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Processing

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

4ffs


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1661 / WRfactor Rwork: 0.1421 / FOM work R set: 0.8841 / SU B: 2.132 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1055 / SU Rfree: 0.1046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1338 5.1 %RANDOM
Rwork0.1583 25024 --
obs0.1598 25024 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.77 Å2 / Biso mean: 19.999 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 24 222 2002
Biso mean--16.46 30.69 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191828
X-RAY DIFFRACTIONr_bond_other_d0.0010.021790
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9772467
X-RAY DIFFRACTIONr_angle_other_deg0.73734139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4815233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62625.67674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.846153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_mcbond_it0.9211.778926
X-RAY DIFFRACTIONr_mcbond_other0.9111.776925
X-RAY DIFFRACTIONr_mcangle_it1.4842.6611158
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 83 -
Rwork0.182 1806 -
all-1889 -
obs--100 %

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