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- PDB-6sun: Amicoumacin kinase hAmiN in complex with AMP-PNP, Ca2+ and Ami -

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Basic information

Entry
Database: PDB / ID: 6sun
TitleAmicoumacin kinase hAmiN in complex with AMP-PNP, Ca2+ and Ami
ComponentsAPH domain-containing protein, amicoumacin kinase
KeywordsANTIMICROBIAL PROTEIN / KINASE / AMICOUMACIN
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Amicoumacin A / :
Function and homology information
Biological speciesBacillus pumilus (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
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APH domain-containing protein, amicoumacin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5285
Polymers39,5181
Non-polymers1,0104
Water6,359353
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-28 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.640, 54.460, 64.630
Angle α, β, γ (deg.)90.000, 113.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein APH domain-containing protein, amicoumacin kinase


Mass: 39517.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank: QENO00000000.1 / Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BW16_03450 / Production host: Escherichia coli (E. coli) / References: UniProt: W8QKP2, EC: 2.7.1.230
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C20H29N3O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 Ca2+

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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: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019 / Details: Be CRLs
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→60 Å / Num. obs: 88781 / % possible obs: 97 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.089 / Net I/σ(I): 13.5
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.77 / Mean I/σ(I) obs: 2 / Num. unique obs: 6187 / CC1/2: 0.681 / Rrim(I) all: 2.87 / % possible all: 95

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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→59.37 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.88 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 4362 5.1 %RANDOM
Rwork0.1415 ---
obs0.1433 81731 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.02 Å2 / Biso mean: 26.422 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0 Å2-0.75 Å2
2--1.27 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.35→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 63 353 3180
Biso mean--20.54 36.93 -
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192959
X-RAY DIFFRACTIONr_bond_other_d0.0020.022730
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9674032
X-RAY DIFFRACTIONr_angle_other_deg1.07636287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54323.907151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28815503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3161516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02734
X-RAY DIFFRACTIONr_rigid_bond_restr5.53635689
X-RAY DIFFRACTIONr_sphericity_free23.6995224
X-RAY DIFFRACTIONr_sphericity_bonded11.48455732
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 305 -
Rwork0.258 5879 -
all-6184 -
obs--95.04 %

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