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

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Basic information

Entry
Database: PDB / ID: 4wkp
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with 2-(2-hydroxyethoxy)ethylthiomethyl-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 / L-methionine salvage from S-adenosylmethionine / methylthioadenosine nucleosidase activity / 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-3QA / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 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 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

Downloads & links

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
B: Aminodeoxyfutalosine nucleosidase
C: Aminodeoxyfutalosine nucleosidase
D: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,26610
Polymers107,5484
Non-polymers1,7186
Water11,908661
1
A: Aminodeoxyfutalosine nucleosidase
B: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7296
Polymers53,7742
Non-polymers9554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-31 kcal/mol
Surface area17110 Å2
MethodPISA
2
C: Aminodeoxyfutalosine nucleosidase
D: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5374
Polymers53,7742
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-52 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.706, 74.078, 176.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 4
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-3QA / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(2-{[2-(2-hydroxyethoxy)ethyl]sulfanyl}ethyl)pyrrolidin-3-ol / 2-(2-hydroxyethoxy)ethylthiomethyl-DADMe-Immucillin-A


Mass: 381.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N5O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.21 Å3/Da / Density % sol: 44.28 % / Description: Rods
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mg/mL); Reservoir (0.2 M sodium fluoride 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 20, 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: 1.58→50 Å / Num. obs: 128267 / % possible obs: 98.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.28 / Net I/av σ(I): 22.714 / Net I/σ(I): 7.8 / Num. measured all: 1005870
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.58-1.617.30.8742.2761010.92694.3
1.61-1.648.10.80363910.951100
1.64-1.678.10.68164730.956100
1.67-1.78.10.55964310.982100
1.7-1.748.10.49964350.997100
1.74-1.788.10.43264741.023100
1.78-1.828.10.36464561.035100
1.82-1.878.10.30664711.104100
1.87-1.9380.2864471.811100
1.93-1.998.10.23864921.236100
1.99-2.068.20.15464841.224100
2.06-2.148.20.13164851.232100
2.14-2.246.50.13662671.50396.4
2.24-2.366.60.11964101.63898.4
2.36-2.518.20.09565101.395100
2.51-2.78.10.08465531.58100
2.7-2.978.10.0865701.697100
2.97-3.480.06566021.682100
3.4-4.296.80.04952861.46279.3
4.29-507.80.04469291.29399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ffs


Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2015 / WRfactor Rwork: 0.1739 / FOM work R set: 0.848 / SU B: 1.619 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0882 / SU Rfree: 0.0878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / SU Rfree Cruickshank DPI: 0.0878 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 6438 5 %RANDOM
Rwork0.1845 121480 --
obs0.1859 121480 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.31 Å2 / Biso mean: 15.966 Å2 / Biso min: 7.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.47 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7017 0 118 661 7796
Biso mean--16.19 22.52 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197323
X-RAY DIFFRACTIONr_bond_other_d0.0010.027202
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9829876
X-RAY DIFFRACTIONr_angle_other_deg0.753316661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83825.586290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.842151321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2591512
X-RAY DIFFRACTIONr_chiral_restr0.0720.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021565
X-RAY DIFFRACTIONr_mcbond_it0.7911.4343690
X-RAY DIFFRACTIONr_mcbond_other0.7891.4343689
X-RAY DIFFRACTIONr_mcangle_it1.2862.1484609
LS refinement shellResolution: 1.584→1.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 498 -
Rwork0.235 8830 -
all-9328 -
obs--98.62 %

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