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- PDB-8i8h: Crystal structure of Cph001-D189N in complex with VIO and ATP -

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Basic information

Entry
Database: PDB / ID: 8i8h
TitleCrystal structure of Cph001-D189N in complex with VIO and ATP
Components
  • KBE-DPP-SER-SER-UAL-5OH
  • Viomycin kinase
KeywordsTRANSFERASE / Phosphotransferase / Capreomycin / Cph / Resistance / ATP / viomycin
Function / homology
Function and homology information


viomycin kinase / viomycin kinase activity / GTP binding / ATP binding
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Viomycin / ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Viomycin kinase
Similarity search - Component
Biological speciesStreptosporangium roseum (bacteria)
Streptomyces vinaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChang, C.Y. / Toh, S.I. / Elaine K, J. / Hsiao, P.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49 -026 -MY3 Taiwan
CitationJournal: Commun Biol / Year: 2023
Title: Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin.
Authors: Toh, S.I. / Elaine Keisha, J. / Wang, Y.L. / Pan, Y.C. / Jhu, Y.H. / Hsiao, P.Y. / Liao, W.T. / Chen, P.Y. / Ko, T.M. / Chang, C.Y.
History
DepositionFeb 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Viomycin kinase
A: Viomycin kinase
D: KBE-DPP-SER-SER-UAL-5OH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1945
Polymers61,5813
Non-polymers6132
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.144, 87.364, 88.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Viomycin kinase


Mass: 30438.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptosporangium roseum (bacteria) / Gene: Sros_4606 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2B3F1
#2: Protein/peptide KBE-DPP-SER-SER-UAL-5OH


Type: Oligopeptide / Class: Antibiotic / Mass: 703.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: viomycin / Source: (gene. exp.) Streptomyces vinaceus (bacteria) / Production host: Streptomyces vinaceus (bacteria) / References: Viomycin
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium acetate trihydrate, Polyethylene glycol 4,000, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→30 Å / Num. obs: 40292 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.4
Reflection shellResolution: 2.02→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6107 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC8.0.004refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→29.08 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25197 1996 4.7 %RANDOM
Rwork0.21848 ---
obs0.22013 40292 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.02→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 38 155 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124378
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164088
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6395943
X-RAY DIFFRACTIONr_angle_other_deg0.8481.5569471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.37558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92310684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025150
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02847
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2174.1332279
X-RAY DIFFRACTIONr_mcbond_other3.3014.1322280
X-RAY DIFFRACTIONr_mcangle_it4.7016.1872834
X-RAY DIFFRACTIONr_mcangle_other4.7386.1862834
X-RAY DIFFRACTIONr_scbond_it4.1244.6712099
X-RAY DIFFRACTIONr_scbond_other4.1234.6712100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1396.8063110
X-RAY DIFFRACTIONr_long_range_B_refined8.05958.3444731
X-RAY DIFFRACTIONr_long_range_B_other8.05858.3414732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.071 Å
RfactorNum. reflection% reflection
Rfree0.383 134 -
Rwork0.369 2840 -
obs--96.43 %

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