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- PDB-6sui: AMICOUMACIN KINASE AMIN -

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Basic information

Entry
Database: PDB / ID: 6sui
TitleAMICOUMACIN KINASE AMIN
ComponentsPhosphotransferase enzyme family protein
KeywordsANTIMICROBIAL PROTEIN / KINASE / AMICOUMACIN
Function / homologyhomoserine kinase activity / threonine biosynthetic process / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily / ATP binding / metal ion binding / : / Aminoglycoside phosphotransferase domain-containing protein
Function and homology information
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8264
Polymers39,1111
Non-polymers7153
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.736, 57.736, 273.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-401-

1PE

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Components

#1: Protein Phosphotransferase enzyme family protein


Mass: 39110.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank: QENN00000000.1 / 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
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

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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: 1.6→12 Å / Num. obs: 62412 / % possible obs: 96.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 4295 / CC1/2: 0.585 / Rrim(I) all: 1.41 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→12 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.412 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.079
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2903 4.8 %RANDOM
Rwork0.1547 ---
obs0.157 57141 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.06 Å2 / Biso mean: 30.954 Å2 / Biso min: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 43 307 3101
Biso mean--47.74 43.76 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192907
X-RAY DIFFRACTIONr_bond_other_d0.0020.022732
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9533922
X-RAY DIFFRACTIONr_angle_other_deg1.08936297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66624.118153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38315501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6731516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02706
X-RAY DIFFRACTIONr_rigid_bond_restr3.50135637
X-RAY DIFFRACTIONr_sphericity_free30.5225183
X-RAY DIFFRACTIONr_sphericity_bonded11.96755685
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 204 -
Rwork0.273 4011 -
all-4215 -
obs--94.98 %

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