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- PDB-8i80: Crystal structure of Cph001-D189N -

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Basic information

Entry
Database: PDB / ID: 8i80
TitleCrystal structure of Cph001-D189N
ComponentsViomycin kinase
KeywordsTRANSFERASE / Phosphotransferase / Capreomycin / Cph / Resistance
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Viomycin kinase
Similarity search - Component
Biological speciesStreptosporangium roseum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.Y. / Toh, S.I. / Elaine K, J.
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 2, 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

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Assembly

Deposited unit
B: Viomycin kinase
A: Viomycin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,70312
Polymers60,8772
Non-polymers82610
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint11 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.299, 86.937, 87.015
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 / Mutation: D189N
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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 28419 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.99
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 3.429 / Num. unique obs: 2768 / CC1/2: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC8.0.004refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.486 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24504 1390 5 %RANDOM
Rwork0.19441 ---
obs0.19712 26244 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.3→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 55 188 4452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164069
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.6355852
X-RAY DIFFRACTIONr_angle_other_deg0.3881.5539426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.997552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50410679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02831
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_it2.3013.4772254
X-RAY DIFFRACTIONr_mcbond_other2.2953.4762252
X-RAY DIFFRACTIONr_mcangle_it3.7845.2022806
X-RAY DIFFRACTIONr_mcangle_other3.7845.2022807
X-RAY DIFFRACTIONr_scbond_it2.5513.9092067
X-RAY DIFFRACTIONr_scbond_other2.5513.912068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2385.6853047
X-RAY DIFFRACTIONr_long_range_B_refined6.34748.8934643
X-RAY DIFFRACTIONr_long_range_B_other6.34448.4344626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.357 Å
RfactorNum. reflection% reflection
Rfree0.339 90 -
Rwork0.224 1536 -
obs--78.78 %

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