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

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Basic information

Entry
Database: PDB / ID: 6ays
TitleCrystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hexylthio-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 / 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-HT6 / adenosylhomocysteine nucleosidase / Aminodeoxyfutalosine nucleosidase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
E: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
F: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
G: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
H: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,71821
Polymers210,4998
Non-polymers3,21913
Water30,5891698
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5387
Polymers52,6252
Non-polymers9135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-11 kcal/mol
Surface area17510 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
G: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4145
Polymers52,6252
Non-polymers7893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-19 kcal/mol
Surface area17560 Å2
MethodPISA
3
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
H: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4145
Polymers52,6252
Non-polymers7893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-25 kcal/mol
Surface area17360 Å2
MethodPISA
4
E: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
F: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3524
Polymers52,6252
Non-polymers7272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-21 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.367, 75.288, 90.437
Angle α, β, γ (deg.)87.54, 89.05, 71.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

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
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 26312.426 Da / Num. of mol.: 8
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-HT6 / (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(hexylsulfanyl)methyl]pyrrolidin-3-ol / Hexylthio-DADMe-Immucillin-A


Mass: 363.521 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H29N5OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1698 / 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: 40.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 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: 1.7→90.35 Å / Num. obs: 179940 / % possible obs: 97.3 % / Redundancy: 4.2 % / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8786 / CC1/2: 0.84 / % possible all: 95.7

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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: 1.7→90.35 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.876 / SU B: 2.715 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24786 8797 4.9 %RANDOM
Rwork0.23033 ---
obs0.23119 171111 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.64 Å20.06 Å2
2--0.19 Å20.07 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.7→90.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14049 0 220 1710 15979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914599
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213999
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.99519721
X-RAY DIFFRACTIONr_angle_other_deg0.894332533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25351864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14425.966595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.647152598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0541524
X-RAY DIFFRACTIONr_chiral_restr0.0730.22292
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022788
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_it1.0342.1537360
X-RAY DIFFRACTIONr_mcbond_other1.0342.1527359
X-RAY DIFFRACTIONr_mcangle_it1.7963.2219196
X-RAY DIFFRACTIONr_mcangle_other1.7963.2219197
X-RAY DIFFRACTIONr_scbond_it1.2562.377239
X-RAY DIFFRACTIONr_scbond_other1.2562.377240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1033.47710506
X-RAY DIFFRACTIONr_long_range_B_refined4.37526.96216510
X-RAY DIFFRACTIONr_long_range_B_other4.37526.96116511
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)
11A145900.05
12B145900.05
21A145900.06
22C145900.06
31A145160.06
32D145160.06
41A146080.05
42E146080.05
51A145540.06
52F145540.06
61A145660.07
62G145660.07
71A145660.06
72H145660.06
81B146120.05
82C146120.05
91B145000.06
92D145000.06
101B146060.05
102E146060.05
111B146440.05
112F146440.05
121B146500.05
122G146500.05
131B146160.05
132H146160.05
141C144400.07
142D144400.07
151C145840.06
152E145840.06
161C145760.06
162F145760.06
171C145940.06
172G145940.06
181C145980.05
182H145980.05
191D144640.06
192E144640.06
201D145380.05
202F145380.05
211D144980.07
212G144980.07
221D144780.06
222H144780.06
231E145680.06
232F145680.06
241E146140.06
242G146140.06
251E146020.05
252H146020.05
261F145920.06
262G145920.06
271F145800.05
272H145800.05
281G145740.06
282H145740.06
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 657 -
Rwork0.233 12455 -
obs--95.82 %

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