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- PDB-4h05: Crystal structure of aminoglycoside-3'-phosphotransferase of type VIII -

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Basic information

Entry
Database: PDB / ID: 4h05
TitleCrystal structure of aminoglycoside-3'-phosphotransferase of type VIII
ComponentsAminoglycoside-O-phosphotransferase VIII
KeywordsTRANSFERASE / protein kinase / ATP binding / Aminoglycoside phosphotransferase VIII / aminoglycoside antibiotic / phosphorilation
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 ...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-O-phosphotransferase VIII
Similarity search - Component
Biological speciesStreptomyces rimosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsBoyko, K.M. / Gorbacheva, M.A. / Danilenko, V.N. / Alekseeva, M.G. / Korzhenevskiy, D.A. / Dorovatovskiy, P.V. / Lipkin, A.V. / Popov, V.O.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation.
Authors: Boyko, K.M. / Gorbacheva, M.A. / Korzhenevskiy, D.A. / Alekseeva, M.G. / Mavletova, D.A. / Zakharevich, N.V. / Elizarov, S.M. / Rudakova, N.N. / Danilenko, V.N. / Popov, V.O.
History
DepositionSep 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside-O-phosphotransferase VIII
B: Aminoglycoside-O-phosphotransferase VIII


Theoretical massNumber of molelcules
Total (without water)60,1442
Polymers60,1442
Non-polymers00
Water1,69394
1
A: Aminoglycoside-O-phosphotransferase VIII


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside-O-phosphotransferase VIII


Theoretical massNumber of molelcules
Total (without water)30,0721
Polymers30,0721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.340, 103.340, 53.680
Angle α, β, γ (deg.)90.000, 94.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminoglycoside-O-phosphotransferase VIII


Mass: 30071.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His6 tag / Source: (gene. exp.) Streptomyces rimosus (bacteria) / Strain: ATCC10970 / Gene: AAG11411 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F9M5, kanamycin kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium citrate; 18% PEG20K, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.985 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 29, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionNumber: 208500 / Rmerge(I) obs: 0.106 / D res high: 2.15 Å / Num. obs: 30335 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.152.3548599.910.826
2.32.4297499.910.635
2.42.5249810010.521
2.52.63272910010.395
2.632.81298810010.294
2.813.03275010010.198
3.033.32259910010.118
3.323.71234410010.062
3.714.27204910010.042
4.275.2173599.810.034
5.27.24137399.910.038
7.243081199.910.017
ReflectionResolution: 2.15→28.97 Å / Num. all: 30435 / Num. obs: 30335 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35.081 Å2
Reflection shellResolution: 2.15→2.206 Å / Mean I/σ(I) obs: 2.63 / Num. unique all: 36911 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R78

3r78
PDB Unreleased entry


Resolution: 2.15→28.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2183 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7979 / SU B: 6.962 / SU ML: 0.177 / SU R Cruickshank DPI: 0.254 / SU Rfree: 0.2252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1536 5.1 %RANDOM
Rwork0.1943 ---
obs0.198 30335 99.92 %-
all-30435 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 111.34 Å2 / Biso mean: 38.7243 Å2 / Biso min: 16.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.15 Å2
2---0.14 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 0 94 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194228
X-RAY DIFFRACTIONr_bond_other_d0.0010.022907
X-RAY DIFFRACTIONr_angle_refined_deg2.3481.9635748
X-RAY DIFFRACTIONr_angle_other_deg1.42236967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5555539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39922205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8815643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6921557
X-RAY DIFFRACTIONr_chiral_restr0.1430.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 120 -
Rwork0.263 2033 -
all-2153 -
obs-36911 99.81 %

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