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- PDB-6fzb: AadA in complex with ATP, magnesium and streptomycin -

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Basic information

Entry
Database: PDB / ID: 6fzb
TitleAadA in complex with ATP, magnesium and streptomycin
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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / STREPTOMYCIN / Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKanchugal P, S. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2013-05930 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
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 1, 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.title / _citation_author.name
Revision 1.3Aug 21, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
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_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.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.value / _struct_conn.pdbx_dist_value / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)63,42615
Polymers60,7762
Non-polymers2,65013
Water3,477193
1
A: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8089
Polymers30,3881
Non-polymers1,4218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Streptomycin 3''-adenylyltransferase
hetero molecules


  • defined by author&software
  • 31.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,6176
Polymers30,3881
Non-polymers1,2295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.670, 82.670, 79.860
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: 30387.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Gene: aadA, STM1264 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8ZPX9, streptomycin 3''-adenylyltransferase

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Non-polymers , 7 types, 206 molecules

#2: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A


Mass: 581.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% v/v PEG 500* MME; 10 % w/v PEG 20000, 0.02M DL-Glutamic acid monohydrate; 0.02M DLAlanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine, 0.1M Sodium HEPES-MOPS pH 7.5

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07438 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07438 Å / Relative weight: 1
ReflectionResolution: 2.05→71.6 Å / Num. obs: 38252 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / CC1/2: 0.992 / Rrim(I) all: 0.112 / Net I/σ(I): 13.43
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2660 / CC1/2: 0.552 / Rrim(I) all: 1.784 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g4a

5g4a


Resolution: 2.05→41.335 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.64
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1909 4.99 %Random selection
Rwork0.1743 ---
obs0.1759 38245 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 168 193 4502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134456
X-RAY DIFFRACTIONf_angle_d0.666114
X-RAY DIFFRACTIONf_dihedral_angle_d12.9622686
X-RAY DIFFRACTIONf_chiral_restr0.037716
X-RAY DIFFRACTIONf_plane_restr0.003757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0502-2.10150.33251290.27582589X-RAY DIFFRACTION100
2.1015-2.15830.30711400.26782570X-RAY DIFFRACTION100
2.1583-2.22180.26281350.24362636X-RAY DIFFRACTION100
2.2218-2.29350.22971380.22622561X-RAY DIFFRACTION100
2.2935-2.37550.24711360.21132616X-RAY DIFFRACTION100
2.3755-2.47060.25541350.20662554X-RAY DIFFRACTION100
2.4706-2.5830.21911400.1872645X-RAY DIFFRACTION100
2.583-2.71920.21841360.19062561X-RAY DIFFRACTION100
2.7192-2.88950.23921370.19192602X-RAY DIFFRACTION100
2.8895-3.11250.21151370.19482623X-RAY DIFFRACTION100
3.1125-3.42560.24081360.18732611X-RAY DIFFRACTION100
3.4256-3.9210.18631390.1612570X-RAY DIFFRACTION100
3.921-4.93870.16811350.13172597X-RAY DIFFRACTION100
4.9387-41.34340.17311360.14782601X-RAY DIFFRACTION100
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)
13.491-2.1919-0.61182.335-0.3481.5745-0.17810.0229-0.7012-0.02960.00160.59340.3084-0.14420.17510.39130.0260.05030.3408-0.02060.4493-22.231678.92477.8394
23.2235-1.52110.25812.7093-0.42381.2163-0.05620.0363-0.32460.0393-0.09450.32740.2131-0.15720.13210.44980.05030.07410.332-0.03280.4559-16.832975.766574.4784
32.0671-0.19480.32223.9189-1.80565.9643-0.23860.1975-0.1709-0.43010.09040.59050.2876-0.22890.15920.4326-0.04110.05450.3955-0.02770.5178-5.390377.614860.6186
43.4754-1.0364-1.67023.87250.47774.29590.09550.04790.10820.0022-0.0120.0964-0.3203-0.0935-0.08530.31840.00330.01060.2770.00250.2814-1.811590.132263.345
55.61080.5992-0.86835.60660.54062.638-0.06670.3025-0.6183-0.0952-0.15330.19060.2373-0.11270.18270.27740.02290.0170.4013-0.05190.3424-42.822293.371784.515
64.7746-1.43460.14591.73180.27420.924-0.1512-0.1191-0.63960.0722-0.03490.30790.2621-0.19740.18190.358-0.01780.06610.4701-0.02190.4506-48.511892.721491.7675
74.11241.24392.15953.71450.41647.21090.0707-0.6248-0.57920.4063-0.3673-0.26320.3569-0.48620.30930.4041-0.04980.04390.4179-0.02570.4885-54.111105.7518105.2493
84.4095-0.6401-1.07433.07611.46283.99080.0422-0.0466-0.0026-0.01580.0479-0.1795-0.01040.2366-0.08220.2568-0.01330.01170.2902-0.02040.2788-45.0007115.0749102.5304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 268 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 59 )
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 158 )
7X-RAY DIFFRACTION7chain 'B' and (resid 159 through 182 )
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 268 )

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