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

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Basic information

Entry
Database: PDB / ID: 6fuc
TitleStructure of aminoglycoside phosphotransferase APH(3'')-Id from Streptomyces rimosus ATCC10970
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
Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesStreptomyces rimosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 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 26, 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


Theoretical massNumber of molelcules
Total (without water)29,8431
Polymers29,8431
Non-polymers00
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.370, 77.660, 78.590
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 (bacteria) / Gene: SRIM_08058 / Production host: Escherichia coli (E. coli) / References: UniProt: L8EXH9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6 / Details: 0.1M Tacsimate; 17% PEG3350; 10% sucrose.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.17→55.24 Å / Num. obs: 98425 / % possible obs: 99.4 % / Redundancy: 4.8 % / CC1/2: 0.966 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.091 / Rrim(I) all: 0.207 / Net I/σ(I): 5.7 / Num. measured all: 475347 / Scaling rejects: 1823
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.17-1.1950.39148480.8690.190.43799.4
6.39-55.245.30.2037180.9450.0920.224100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
Aimless0.5.17data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKH

4gkh


Resolution: 1.17→55.24 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.095 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 4751 4.8 %RANDOM
Rwork0.1378 ---
obs0.1394 93604 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.42 Å2 / Biso mean: 16.001 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.17→55.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 0 386 2435
Biso mean---30.65 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192177
X-RAY DIFFRACTIONr_bond_other_d0.0020.021536
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9672962
X-RAY DIFFRACTIONr_angle_other_deg1.08533524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75121.981106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78115348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7081530
X-RAY DIFFRACTIONr_chiral_restr0.150.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_rigid_bond_restr3.4133713
X-RAY DIFFRACTIONr_sphericity_free28.825239
X-RAY DIFFRACTIONr_sphericity_bonded15.0553811
LS refinement shellResolution: 1.167→1.197 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 351 -
Rwork0.168 6849 -
all-7200 -
obs--99.32 %

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