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- PDB-6ayt: Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/... -

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Basic information

Entry
Database: PDB / ID: 6ayt
TitleCrystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with pyrazinylthio-DADMe-Immucillin-A
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / TRANSFERASE / MTAN enzyme / Foodborne Diseases
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-4EH / adenosylhomocysteine nucleosidase / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Transition-State Analogues of Campylobacter jejuni 5'-Methylthioadenosine Nucleosidase.
Authors: Ducati, R.G. / Harijan, R.K. / Cameron, S.A. / Tyler, P.C. / Evans, G.B. / Schramm, V.L.
History
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,86611
Polymers105,2504
Non-polymers1,6167
Water9,170509
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4646
Polymers52,6252
Non-polymers8394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-17 kcal/mol
Surface area17680 Å2
MethodPISA
2
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4025
Polymers52,6252
Non-polymers7773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-21 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.078, 90.983, 72.451
Angle α, β, γ (deg.)90.00, 111.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 228 / Label seq-ID: 10 - 238

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 26312.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0M70_07260, AJY53_05400 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1E7P7U4, UniProt: Q0PC20*PLUS, 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.: 4 / Source method: obtained synthetically / Formula: C16H19N7OS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.1 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM Magnesium Chloride, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 22, 2017
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→67.44 Å / Num. obs: 73146 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4499 / CC1/2: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WKN

4wkn


Resolution: 1.85→67.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.369 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 3703 5.1 %RANDOM
Rwork0.2192 ---
obs0.22053 69342 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-1.08 Å2
2---0.16 Å20 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.85→67.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 112 509 7677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197304
X-RAY DIFFRACTIONr_bond_other_d0.0020.027022
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9999851
X-RAY DIFFRACTIONr_angle_other_deg0.879316313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17425.96297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.991151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7661512
X-RAY DIFFRACTIONr_chiral_restr0.0710.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021399
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_it1.0972.5153666
X-RAY DIFFRACTIONr_mcbond_other1.0972.5143665
X-RAY DIFFRACTIONr_mcangle_it1.8873.7644577
X-RAY DIFFRACTIONr_mcangle_other1.8873.7654578
X-RAY DIFFRACTIONr_scbond_it1.2382.743638
X-RAY DIFFRACTIONr_scbond_other1.2382.743638
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1094.0265272
X-RAY DIFFRACTIONr_long_range_B_refined3.72129.5627966
X-RAY DIFFRACTIONr_long_range_B_other3.7229.5627967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A144540.06
12B144540.06
21A144980.06
22C144980.06
31A145100.05
32D145100.05
41B144320.06
42C144320.06
51B144380.06
52D144380.06
61C145700.04
62D145700.04
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 288 -
Rwork0.303 5127 -
obs--99.96 %

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