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- PDB-6sum: Amicoumacin kinase hAmiN in complex with AMP-PNP, MG2+ and Ami -

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Basic information

Entry
Database: PDB / ID: 6sum
TitleAmicoumacin kinase hAmiN in complex with AMP-PNP, MG2+ and Ami
ComponentsAMICOUMACIN KINASE
KeywordsANTIMICROBIAL PROTEIN / KINASE / AMICOUMACIN
Function / homologyACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Amicoumacin A
Function and homology information
Biological speciesBacillus altitudinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMICOUMACIN KINASE
B: AMICOUMACIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,07512
Polymers79,0362
Non-polymers2,04010
Water14,304794
1
A: AMICOUMACIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5556
Polymers39,5181
Non-polymers1,0375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMICOUMACIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5206
Polymers39,5181
Non-polymers1,0035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.660, 66.000, 70.410
Angle α, β, γ (deg.)112.290, 102.810, 94.790
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AMICOUMACIN KINASE


Mass: 39517.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank: QENO00000000.1 / Source: (gene. exp.) Bacillus altitudinis (bacteria) / Gene: BW16_03450 / Production host: Escherichia coli (E. coli) / References: EC: 2.7.1.230

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Non-polymers , 5 types, 804 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-UAM / Amicoumacin A


Mass: 423.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N3O7
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH6.5 0.2 M NaOAc 27-29% (w/v) PEG 2000MME 2 mM amiA 2.2 mM AMP-PNP 20 mM Mg2+

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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: Jun 12, 2019 / 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: 1.35→12 Å / Num. obs: 177497 / % possible obs: 95.6 % / Redundancy: 6.85 % / Biso Wilson estimate: 14.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Net I/σ(I): 11.1
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 7.07 % / Rmerge(I) obs: 1.091 / Num. unique obs: 12337 / CC1/2: 0.686 / Rrim(I) all: 1.05 / % possible all: 93.7

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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: 1.35→12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.775 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 8575 5.1 %RANDOM
Rwork0.1445 ---
obs0.1461 161039 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 19.436 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.04 Å20.07 Å2
2---0.13 Å2-0.13 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.35→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5559 0 137 788 6484
Biso mean--15.35 30.57 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195988
X-RAY DIFFRACTIONr_bond_other_d0.0020.025552
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9718162
X-RAY DIFFRACTIONr_angle_other_deg1.077312790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80423.803305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.515151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9161535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026737
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021480
X-RAY DIFFRACTIONr_rigid_bond_restr2.562311540
X-RAY DIFFRACTIONr_sphericity_free23.0025471
X-RAY DIFFRACTIONr_sphericity_bonded8.154511683
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 620 -
Rwork0.223 11579 -
all-12199 -
obs--93.78 %

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