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

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Basic information

Entry
Database: PDB / ID: 4wkn
TitleCrystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-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 / 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-TDI / 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
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

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Assembly

Deposited unit
A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1802
Polymers26,8871
Non-polymers2931
Water2,684149
1
A: Aminodeoxyfutalosine nucleosidase
hetero molecules

A: Aminodeoxyfutalosine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3614
Polymers53,7742
Non-polymers5872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_555-x,-z,-y1
Buried area4660 Å2
ΔGint-26 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.958, 156.958, 156.958
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-426-

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-TDI / (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL / (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE


Mass: 293.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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 Å3/Da / Density % sol: 58.95 % / Description: cubes
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein (10 mg/mL); Reservoir (0.1 M Bicine pH 9.0 and 2.4 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: 2→50 Å / Num. obs: 22676 / % possible obs: 100 % / Redundancy: 39.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.018 / Rrim(I) all: 0.117 / Χ2: 1.04 / Net I/av σ(I): 44.978 / Net I/σ(I): 7.2 / Num. measured all: 903055
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
2-2.03380.8115.7911170.9660.1330.8220.777100
2.03-2.0737.90.70611080.9720.1150.7150.854100
2.07-2.1138.40.66411080.9760.1080.6730.84100
2.11-2.1538.50.5411250.9880.0880.5470.827100
2.15-2.238.60.4611000.990.0750.4660.848100
2.2-2.2538.80.43811160.9910.0710.4440.926100
2.25-2.3138.80.38311240.9920.0620.3880.892100
2.31-2.37390.33811100.9930.0550.3430.877100
2.37-2.44390.30511240.9940.0490.3090.875100
2.44-2.5239.40.26911250.9960.0430.2720.897100
2.52-2.6139.70.21210970.9970.0340.2140.918100
2.61-2.7140.10.18511400.9980.0290.1880.972100
2.71-2.8440.90.15811220.9990.0250.160.98100
2.84-2.9941.80.13511320.9990.0210.1371.028100
2.99-3.1742.20.1111340.9990.0170.1111.225100
3.17-3.4242.40.0911490.9990.0140.0911.517100
3.42-3.7641.80.07114610.0110.071.433100
3.76-4.3140.80.051115010.0080.0521.472100
4.31-5.4340.60.04118510.0060.0411.343100
5.43-5039.70.034126410.0050.0351.0999.8

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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: 2→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1585 / WRfactor Rwork: 0.1438 / FOM work R set: 0.8744 / SU B: 5.032 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1241 / SU Rfree: 0.1095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.109 / SU Rfree Cruickshank DPI: 0.1095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 1159 5.1 %RANDOM
Rwork0.1616 21462 --
obs0.1625 21409 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.48 Å2 / Biso mean: 25.386 Å2 / Biso min: 14.39 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 20 149 1922
Biso mean--19.42 31.55 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191837
X-RAY DIFFRACTIONr_bond_other_d0.0010.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9752484
X-RAY DIFFRACTIONr_angle_other_deg0.74734148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52125.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33515329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.097153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_mcbond_it0.7091.678933
X-RAY DIFFRACTIONr_mcbond_other0.6991.677932
X-RAY DIFFRACTIONr_mcangle_it1.1122.5131169
LS refinement shellResolution: 1.998→2.05 Å
RfactorNum. reflection% reflection
Rfree0.221 78 -
Rwork0.19 1538 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.0896 Å / Origin y: 45.0353 Å / Origin z: -26.3273 Å
111213212223313233
T0.0356 Å2-0.0026 Å20.0023 Å2-0.0121 Å2-0.0183 Å2--0.0331 Å2
L1.4586 °20.0725 °20.544 °2-0.9274 °2-0.0162 °2--1.14 °2
S-0.0342 Å °-0.1141 Å °0.1983 Å °0.0912 Å °0.0162 Å °-0.0197 Å °-0.171 Å °0.0032 Å °0.018 Å °

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