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- PDB-5g4a: AadA in complex with ATP and magnesium -

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Basic information

Entry
Database: PDB / ID: 5g4a
TitleAadA in complex with ATP and magnesium
Components(Aminoglycoside (3'') (9) ...) x 2
KeywordsTRANSFERASE / AMINOGLYCOSIDE ADENYL TRANSFERASE / ANT(3'')9 / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function
Adenylyltransferase AadA/Aad9 / Adenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Aminoglycoside (3'') (9) adenylyltransferase / Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStern, A.L. / van der Verren, S. / Selmer, M.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase fromSalmonella enterica.
Authors: Stern, A.L. / Van der Verren, S.E. / Kanchugal P, S. / Nasvall, J. / Gutierrez-de-Teran, H. / Selmer, M.
History
DepositionMay 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_mod_residue.details / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside (3'') (9) adenylyltransferase
B: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,67525
Polymers61,1762
Non-polymers2,49823
Water9,548530
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A: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,79712
Polymers30,6041
Non-polymers1,19311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,87713
Polymers30,5721
Non-polymers1,30512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.330, 82.330, 79.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Aminoglycoside (3'') (9) ... , 2 types, 2 molecules AB

#1: Protein Aminoglycoside (3'') (9) adenylyltransferase


Mass: 30604.154 Da / Num. of mol.: 1
Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: ENTERICA SEROVAR TYPHIMURIUM STR. LT2 / Gene: aadA / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0W4NPT0, UniProt: Q8ZPX9*PLUS
#2: Protein Aminoglycoside (3'') (9) adenylyltransferase


Mass: 30572.088 Da / Num. of mol.: 1
Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: ENTERICA SEROVAR TYPHIMURIUM STR. LT2 / Gene: aadA / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0W4NPT0, UniProt: Q8ZPX9*PLUS

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Non-polymers , 8 types, 553 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 103.120 Da / Num. of mol.: 6 / Source method: obtained synthetically
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE

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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growpH: 8.5
Details: 10% W/V PEG 20 000, 20% V/V PEG MME 550, 0.1 M BICINE/TRIZMA BASE PH 8.5, 0.02 M EACH OF SODIUM L-GLUTAMATE, DL-ALANINE, GLYCINE, DL-LYSINE HCL AND DL-SERINE (MORPHEUS SCREEN, MOLECULAR DIMENSIONS)

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 28, 2014 / Details: PT COATED MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→41.165 Å / Num. obs: 46215 / % possible obs: 96.9 % / Observed criterion σ(I): -0.3 / Redundancy: 9.7 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.52 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CS6

4cs6


Resolution: 1.9→41.165 Å / SU ML: 0.26 / σ(F): 2.39 / Phase error: 25.11 / Stereochemistry target values: ML
Details: THERE IS WEAK UN-MODELLED DENSITY FOR THE C-TERMINAL HEXAHISTIDINE TAG. WATER MOLECULES A2130, A2131, A2044 AND B2032, B2101, B2102 ARE MODELLED IN DENSITY THAT MAY REPRESENT AN UNKNOWN LIGAND.
RfactorNum. reflection% reflection
Rfree0.2222 2337 5 %
Rwork0.1761 --
obs0.1784 46747 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 119 530 4795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074496
X-RAY DIFFRACTIONf_angle_d0.9076154
X-RAY DIFFRACTIONf_dihedral_angle_d12.242727
X-RAY DIFFRACTIONf_chiral_restr0.05695
X-RAY DIFFRACTIONf_plane_restr0.005809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93880.53471180.51472223X-RAY DIFFRACTION84
1.9388-1.98090.31691390.28352655X-RAY DIFFRACTION100
1.9809-2.0270.27011370.23082600X-RAY DIFFRACTION100
2.027-2.07770.25981410.21572667X-RAY DIFFRACTION100
2.0777-2.13390.28171370.2022618X-RAY DIFFRACTION100
2.1339-2.19670.25861430.20572708X-RAY DIFFRACTION100
2.1967-2.26760.32751340.27922537X-RAY DIFFRACTION98
2.2676-2.34860.21561390.18332647X-RAY DIFFRACTION100
2.3486-2.44260.21531390.16992638X-RAY DIFFRACTION100
2.4426-2.55380.2041390.16822635X-RAY DIFFRACTION100
2.5538-2.68840.2391390.17032639X-RAY DIFFRACTION100
2.6884-2.85680.21771400.17022665X-RAY DIFFRACTION100
2.8568-3.07730.21241370.17142614X-RAY DIFFRACTION100
3.0773-3.38680.19551390.15982631X-RAY DIFFRACTION100
3.3868-3.87660.21461400.14522653X-RAY DIFFRACTION100
3.8766-4.88290.17451390.12782646X-RAY DIFFRACTION100
4.8829-41.17460.16631370.14292634X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.9525 Å / Origin y: 71.339 Å / Origin z: 56.9177 Å
111213212223313233
T0.1142 Å20.0011 Å20.0032 Å2-0.1148 Å20.0008 Å2--0.1429 Å2
L-0.091 °20.0148 °20.0207 °2-0.4365 °20.342 °2--0.4338 °2
S-0.0425 Å °-0.0005 Å °-0.0042 Å °-0.0001 Å °-0.0079 Å °0.1525 Å °-0.0024 Å °-0.0651 Å °-0.0001 Å °
Refinement TLS groupSelection details: ALL

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