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- PDB-5lpa: AadA E87Q in complex with ATP, calcium and dihydrostreptomycin -

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Basic information

Entry
Database: PDB / ID: 5lpa
TitleAadA E87Q in complex with ATP, calcium and dihydrostreptomycin
ComponentsStreptomycin 3''-adenylyltransferase
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
dihydrostreptomycin / ADENOSINE-5'-TRIPHOSPHATE / Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStern, A.L. / Van der Verren, S.E. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg FoundationRiboCORE Sweden
Citation
Journal: 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.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase.
Authors: Chen, Y. / Nasvall, J. / Wu, S. / Andersson, D.I. / Selmer, M.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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
Revision 1.2Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptomycin 3''-adenylyltransferase
B: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82915
Polymers61,2302
Non-polymers2,59913
Water12,556697
1
A: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8847
Polymers30,6151
Non-polymers1,2686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9468
Polymers30,6151
Non-polymers1,3317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.885, 82.885, 79.782
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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Protein , 1 types, 2 molecules AB

#1: Protein Streptomycin 3''-adenylyltransferase


Mass: 30615.158 Da / Num. of mol.: 2 / Mutation: E87Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: aadA, STM1264 / Plasmid: PEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8ZPX9, streptomycin 3''-adenylyltransferase

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Non-polymers , 6 types, 710 molecules

#2: 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
#3: Chemical ChemComp-71R / dihydrostreptomycin


Mass: 583.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41N7O12 / Comment: antibiotic*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000, 0.2 M Calcium chloride, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.4→41.442 Å / Num. obs: 120821 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.19 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.4
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 5.18 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.14 / CC1/2: 0.727 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g4a

5g4a


Resolution: 1.4→41.442 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 5960 4.94 %Random selection
Rwork0.146 ---
obs0.1476 120743 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 160 697 5088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144804
X-RAY DIFFRACTIONf_angle_d1.3816616
X-RAY DIFFRACTIONf_dihedral_angle_d15.7631850
X-RAY DIFFRACTIONf_chiral_restr0.099756
X-RAY DIFFRACTIONf_plane_restr0.008872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.26732000.22313839X-RAY DIFFRACTION100
1.4159-1.43260.2481820.21943846X-RAY DIFFRACTION100
1.4326-1.450.23962080.20223874X-RAY DIFFRACTION100
1.45-1.46840.25272060.1893745X-RAY DIFFRACTION100
1.4684-1.48770.25641940.18183819X-RAY DIFFRACTION100
1.4877-1.50810.20531600.17283929X-RAY DIFFRACTION100
1.5081-1.52970.22782260.16363735X-RAY DIFFRACTION100
1.5297-1.55250.23752200.16153806X-RAY DIFFRACTION100
1.5525-1.57670.20341880.15783914X-RAY DIFFRACTION100
1.5767-1.60260.19412020.14333766X-RAY DIFFRACTION100
1.6026-1.63020.18561760.13023860X-RAY DIFFRACTION100
1.6302-1.65990.17361790.12533832X-RAY DIFFRACTION100
1.6599-1.69180.16842160.12023849X-RAY DIFFRACTION100
1.6918-1.72630.15811840.11283816X-RAY DIFFRACTION100
1.7263-1.76390.1612300.1193799X-RAY DIFFRACTION100
1.7639-1.80490.18281720.12013849X-RAY DIFFRACTION100
1.8049-1.850.15072100.12133813X-RAY DIFFRACTION100
1.85-1.90010.16751940.13483821X-RAY DIFFRACTION100
1.9001-1.9560.19282120.13593815X-RAY DIFFRACTION100
1.956-2.01910.17361740.12653886X-RAY DIFFRACTION100
2.0191-2.09130.15262160.12513791X-RAY DIFFRACTION100
2.0913-2.1750.18821860.13823837X-RAY DIFFRACTION100
2.175-2.2740.17141470.13263852X-RAY DIFFRACTION100
2.274-2.39390.18062160.13963826X-RAY DIFFRACTION100
2.3939-2.54380.17491840.14513799X-RAY DIFFRACTION100
2.5438-2.74020.17772010.15013881X-RAY DIFFRACTION100
2.7402-3.01590.17512100.16063782X-RAY DIFFRACTION100
3.0159-3.45210.18152230.15593802X-RAY DIFFRACTION100
3.4521-4.34850.15312200.14493816X-RAY DIFFRACTION100
4.3485-41.46060.16982240.15593784X-RAY DIFFRACTION100

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