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- PDB-6fux: Structure of aminoglycoside phosphotransferase APH(3'')-Id from S... -

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Basic information

Entry
Database: PDB / ID: 6fux
TitleStructure of aminoglycoside phosphotransferase APH(3'')-Id from Streptomyces rimosus ATCC10970 in complex with ADP and streptomycin
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / Streptomyces rimosus / aminoglycoside phosphotransferase / antibiotic resistance / streptomycin / phosphorylation / ATP binding / kinase activity
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / kinase activity / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function
Aminoglycoside 3-phosphotransferase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / STREPTOMYCIN / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesStreptomyces rimosus subsp. rimosus ATCC 10970 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Korzhenevskiy, D.A. / Alekseeva, M.G. / Mavletova, D.A. / Zakharevich, N.V. / Rudakova, N.N. / Danilenko, V.N. / Popov, V.O.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
Russian Science Foundation17-04-01106 Russian Federation
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: Identification, functional and structural characterization of novel aminoglycoside phosphotransferase APH(3′′)-Id from Streptomyces rimosus subsp. rimosus ATCC 10970.
Authors: Alekseeva, M.G. / Boyko, K.M. / Nikolaeva, A.Y. / Mavletova, D.A. / Rudakova, N.N. / Zakharevich, N.V. / Korzhenevskiy, D.A. / Ziganshin, R.H. / Popov, V.O. / Danilenko, V.N.
History
DepositionFeb 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9444
Polymers29,8431
Non-polymers1,1013
Water4,720262
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.970, 77.800, 78.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminoglycoside phosphotransferase


Mass: 29843.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimosus subsp. rimosus ATCC 10970 (bacteria)
Gene: SRIM_08058 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L8EXH9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES monohydrate; 12% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→55.3 Å / Num. obs: 34969 / % possible obs: 98.8 % / Redundancy: 5.952 % / Biso Wilson estimate: 27.329 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.151 / Χ2: 0.958 / Net I/σ(I): 8.04 / Num. measured all: 208148
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.76.1970.6512.229270.8250.7198.2
1.7-1.85.9370.4813.0749510.9020.52798.7
1.8-26.2350.3445.0772200.9550.37598.9
2-2.55.9570.2088.995540.9810.22899
2.5-35.7490.14211.6542610.980.15799
3-45.5860.10813.9234190.9880.11998.4
4-105.7510.09215.424420.9910.10198.8
10-505.4070.07615.731940.9920.08499.5
50-55.340.02614.2110.03100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FUC

6fuc


Resolution: 1.65→55.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.027 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0914 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.092
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 1740 5 %RANDOM
Rwork0.1683 ---
obs0.1699 33229 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.54 Å2 / Biso mean: 28.84 Å2 / Biso min: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---2.17 Å20 Å2
3---2.69 Å2
Refinement stepCycle: final / Resolution: 1.65→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 66 262 2387
Biso mean--40.53 39.29 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0142230
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171925
X-RAY DIFFRACTIONr_angle_refined_deg2.761.7023045
X-RAY DIFFRACTIONr_angle_other_deg2.5191.6614533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8265265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.54319.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26515335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3031529
X-RAY DIFFRACTIONr_chiral_restr0.4160.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022549
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02418
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 115 -
Rwork0.267 2424 -
all-2539 -
obs--98.11 %
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)
10.81370.1731-0.47570.9096-0.09521.07830.0447-0.11460.03350.134-0.0054-0.0734-0.05070.0597-0.03920.021-0.0042-0.0090.1458-0.00870.009330.617765.412517.6273
213.4715-16.691519.379160.8101-41.819135.78041.3698-0.15590.57820.5221-2.2919-0.91830.97760.87580.9220.3866-0.10520.03520.1782-0.00360.077637.699164.671810.1978
30.48160.0982-0.20820.6808-0.03630.91470.0369-0.01990.00170.062-0.0268-0.04380.00110.0353-0.01010.12790.0047-0.02550.2638-0.00680.115430.12564.786216.8299
42.8245-1.16156.90062.263-7.672329.96540.1081-0.1427-0.0084-0.0173-0.1151-0.0080.2240.14940.0070.11330.0199-0.00140.1197-0.00310.087339.780170.212612.6924
59.50844.566310.68752.2645.022512.19780.0566-0.14920.08920.2061-0.13490.0281-0.2008-0.02790.07830.4647-0.1159-0.06260.1984-0.08950.176133.921668.871927.2241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 272
2X-RAY DIFFRACTION2A301
3X-RAY DIFFRACTION3A401 - 662
4X-RAY DIFFRACTION4A302
5X-RAY DIFFRACTION5A303

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