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- PDB-5ue1: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 5ue1
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE / NUCLEAR PROTEIN
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine
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
9-DEAZAADENINE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
Revision 1.2Feb 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62315
Polymers49,7512
Non-polymers87213
Water12,160675
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.642, 72.915, 57.563
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: -1 - 231 / Label seq-ID: 2 - 234

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99739, -0.072177, 0.0019), (-0.072202, 0.997151, -0.021858), (-0.000317, -0.021938, -0.999759)99.76464, 4.82419, 108.53557

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase ...MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase / SRH nucleosidase


Mass: 24875.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: mtnN, VF_2128 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: Q5E2X3, adenosylhomocysteine nucleosidase

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Non-polymers , 6 types, 688 molecules

#2: Chemical ChemComp-9DA / 9-DEAZAADENINE


Mass: 134.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M CaCl2, 0.1 M HEPES, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2016 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.14→30 Å / Num. obs: 144464 / % possible obs: 92.2 % / Redundancy: 4.4 % / CC1/2: 0.79 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.2
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 7077 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DP9

3dp9


Resolution: 1.14→30 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.032 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15785 7428 5.1 %RANDOM
Rwork0.12911 ---
obs0.13059 137008 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0.16 Å2
2---0.37 Å20 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.14→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 48 682 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193827
X-RAY DIFFRACTIONr_bond_other_d0.0020.023583
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9685227
X-RAY DIFFRACTIONr_angle_other_deg1.11638344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65126150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6481511
X-RAY DIFFRACTIONr_chiral_restr0.2890.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02714
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_it1.2990.9962013
X-RAY DIFFRACTIONr_mcbond_other1.2962010
X-RAY DIFFRACTIONr_mcangle_it1.6071.5072554
X-RAY DIFFRACTIONr_mcangle_other1.6072555
X-RAY DIFFRACTIONr_scbond_it2.5731814
X-RAY DIFFRACTIONr_scbond_other2.5691814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.862674
X-RAY DIFFRACTIONr_long_range_B_refined4.0214500
X-RAY DIFFRACTIONr_long_range_B_other3.9324438
X-RAY DIFFRACTIONr_rigid_bond_restr4.96633813
X-RAY DIFFRACTIONr_sphericity_free20.895132
X-RAY DIFFRACTIONr_sphericity_bonded10.48553842
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3211 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.235
Bloose thermal2.1810
LS refinement shellResolution: 1.141→1.171 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 540 -
Rwork0.224 9794 -
obs--89.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71390.2157-0.14581.32970.28750.86520.0439-0.0490.02460.0281-0.0290.0389-0.0951-0.0508-0.01490.041-0.00090.00760.0244-0.00320.002845.98436.204470.7568
20.2901-0.098-0.26730.16330.15630.90230.0026-0.0302-0.0080.003-0.0365-0.02970.03390.11010.03390.02580.00250.00250.0390.01970.011356.1939-7.873762.3461
31.78690.6014-2.10730.9822-0.73474.6925-0.0124-0.07670.01380.09140.0385-0.06280.0140.1368-0.02610.02150.0014-0.01180.0198-0.0020.00860.943-2.668979.9775
40.23510.1155-0.18070.5352-0.01040.9938-0.0257-0.0368-0.020.0183-0.0386-0.03010.13450.09520.06430.03780.00750.00830.0170.00830.005852.6381-11.62769.7012
50.6019-0.1488-0.12531.2883-0.24030.91870.030.06630.0301-0.0296-0.0095-0.0389-0.09380.0107-0.02050.03760.00610.00850.02430.00590.003953.60946.074537.5933
60.32610.1729-0.10380.2518-0.23450.79830.00520.0538-0.00130.0025-0.01620.02540.0336-0.13210.0110.027-0.00540.00480.0701-0.01880.007344.3779-8.477846.3287
73.2158-0.777-2.96611.18450.98825.3879-0.01090.18420.0238-0.1339-0.00150.0798-0.0097-0.21430.01240.0231-0.0013-0.01190.04290.00340.007638.4587-3.51229.1835
80.38590.0425-0.17310.3284-0.20330.7436-0.0330.0784-0.0324-0.0541-0.0175-0.00140.1208-0.13150.05050.0435-0.01050.00850.0464-0.01390.005248.2964-12.493539.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 48
2X-RAY DIFFRACTION2A49 - 121
3X-RAY DIFFRACTION3A122 - 139
4X-RAY DIFFRACTION4A140 - 231
5X-RAY DIFFRACTION5B-1 - 48
6X-RAY DIFFRACTION6B49 - 121
7X-RAY DIFFRACTION7B122 - 138
8X-RAY DIFFRACTION8B139 - 230

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