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- PDB-6sv5: Amicoumacin kinase AmiN in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 6sv5
TitleAmicoumacin kinase AmiN in complex with ATP
ComponentsPhosphotransferase enzyme family protein, amicoumacin kinase
KeywordsANTIMICROBIAL PROTEIN / KINASE / AMICOUMACIN
Function / homology
Function and homology information


homoserine kinase activity / threonine biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / 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'-TRIPHOSPHATE / : / Aminoglycoside phosphotransferase domain-containing protein
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBourenkov, G.P. / Mokrushina, Y.A. / Terekhov, S.S. / Smirnov, I.V. / Gabibov, A.G. / Altman, S.
Funding support Russian Federation, 3items
OrganizationGrant numberCountry
Russian Science Foundation19-14-00331 Russian Federation
Russian Foundation for Basic Research19-34-70021 Russian Federation
Russian Foundation for Basic Research18-29-08054 Russian Federation
CitationJournal: Sci Adv / Year: 2020
Title: A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding.
Authors: Terekhov, S.S. / Mokrushina, Y.A. / Nazarov, A.S. / Zlobin, A. / Zalevsky, A. / Bourenkov, G. / Golovin, A. / Belogurov Jr., A. / Osterman, I.A. / Kulikova, A.A. / Mitkevich, V.A. / Lou, H.J. ...Authors: Terekhov, S.S. / Mokrushina, Y.A. / Nazarov, A.S. / Zlobin, A. / Zalevsky, A. / Bourenkov, G. / Golovin, A. / Belogurov Jr., A. / Osterman, I.A. / Kulikova, A.A. / Mitkevich, V.A. / Lou, H.J. / Turk, B.E. / Wilmanns, M. / Smirnov, I.V. / Altman, S. / Gabibov, A.G.
History
DepositionSep 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Phosphotransferase enzyme family protein, amicoumacin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6182
Polymers39,1111
Non-polymers5071
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-3 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.277, 58.277, 281.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphotransferase enzyme family protein, amicoumacin kinase


Mass: 39110.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: C6X97_15155, EJB14_06995 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2T0D6W6, UniProt: A8FAR5*PLUS, EC: 2.7.1.230
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, pH 8.5 2.5-2.65 M ammonium sulfate 10 mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 20, 2018 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→70.5 Å / Num. obs: 34143 / % possible obs: 97.23 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 2366 / CC1/2: 0.987 / Rrim(I) all: 0.229

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.574 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1713 5.2 %RANDOM
Rwork0.2074 ---
obs0.209 31484 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.57 Å2 / Biso mean: 32.7 Å2 / Biso min: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å2-0 Å2
2--1.49 Å2-0 Å2
3----2.99 Å2
Refinement stepCycle: final / Resolution: 2→70.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 31 209 2948
Biso mean--54.67 34.6 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192848
X-RAY DIFFRACTIONr_bond_other_d0.0030.022624
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9593859
X-RAY DIFFRACTIONr_angle_other_deg1.13136043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61824.371151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85215487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0561514
X-RAY DIFFRACTIONr_chiral_restr0.1270.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 114 -
Rwork0.262 2243 -
all-2357 -
obs--96.6 %
Refinement TLS params.Method: refined / Origin x: 6.301 Å / Origin y: 16.774 Å / Origin z: 17.886 Å
111213212223313233
T0.001 Å20.0001 Å2-0.0081 Å2-0.2256 Å20.0328 Å2--0.2336 Å2
L0.1995 °2-0.0421 °2-0.1962 °2-0.0162 °20.0608 °2--0.2567 °2
S0.0093 Å °-0.0097 Å °0.0031 Å °-0.0035 Å °0.0035 Å °0.0078 Å °-0.0125 Å °-0.0327 Å °-0.0128 Å °

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