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

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Basic information

Entry
Database: PDB / ID: 6ayr
TitleCrystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-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 / 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-BIG / adenosylhomocysteine nucleosidase / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.1Oct 31, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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)106,77811
Polymers105,2504
Non-polymers1,5287
Water4,810267
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3585
Polymers52,6252
Non-polymers7333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-21 kcal/mol
Surface area18060 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4206
Polymers52,6252
Non-polymers7954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-21 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.156, 91.407, 78.431
Angle α, β, γ (deg.)90.00, 109.97, 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-BIG / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol / butylthio-DADMe-Immucillin A


Mass: 335.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N5OS
#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.: 267 / 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: 43.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 800 mM Lithium Chloride, 32% (w/v) PEG 4000

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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: 1.95→73.72 Å / Num. obs: 65501 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.99 / Net I/σ(I): 11.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4607 / CC1/2: 0.66 / % possible all: 99.9

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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: 1.95→73.72 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.012 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 3289 5 %RANDOM
Rwork0.22347 ---
obs0.22497 62193 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å22.34 Å2
2---2.9 Å20 Å2
3---1.35 Å2
Refinement stepCycle: 1 / Resolution: 1.95→73.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 104 267 7423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197273
X-RAY DIFFRACTIONr_bond_other_d0.0020.027025
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9969802
X-RAY DIFFRACTIONr_angle_other_deg0.933316316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24325.946296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.968151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3851512
X-RAY DIFFRACTIONr_chiral_restr0.0790.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
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_it1.954.2133660
X-RAY DIFFRACTIONr_mcbond_other1.9494.2123659
X-RAY DIFFRACTIONr_mcangle_it3.0316.3094568
X-RAY DIFFRACTIONr_mcangle_other3.0316.314569
X-RAY DIFFRACTIONr_scbond_it2.0834.5043613
X-RAY DIFFRACTIONr_scbond_other2.0834.5043613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3566.6475235
X-RAY DIFFRACTIONr_long_range_B_refined4.93748.6997690
X-RAY DIFFRACTIONr_long_range_B_other4.93848.6997691
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)
11A141680.06
12B141680.06
21A139860.08
22C139860.08
31A139840.08
32D139840.08
41B140700.07
42C140700.07
51B140020.07
52D140020.07
61C139080.08
62D139080.08
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 252 -
Rwork0.332 4594 -
obs--99.92 %

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