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- PDB-8i82: Crystal structure of Cph001-D189N in complex with CMN IIA -

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Basic information

Entry
Database: PDB / ID: 8i82
TitleCrystal structure of Cph001-D189N in complex with CMN IIA
Components
  • KBE-DPP-UAL-MYN-DPP-SER
  • Viomycin 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
Capreomycin IA / ACETATE ION / Viomycin kinase
Similarity search - Component
Biological speciesStreptosporangium roseum (bacteria)
Saccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 3, 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-UAL-MYN-DPP-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7416
Polymers61,5643
Non-polymers1773
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-0 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.334, 84.492, 86.778
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-UAL-MYN-DPP-SER


Type: Cyclic peptide / Class: Inhibitor / Mass: 686.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CMN IIA
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Production host: Saccharothrix mutabilis subsp. capreolus (bacteria)
References: Capreomycin IA
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
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: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 44947 / % possible obs: 99.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 35.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 4338 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC8.0.004refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.87 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24863 2368 5.8 %RANDOM
Rwork0.19158 ---
obs0.19489 38338 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.739 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.95→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 12 376 4644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164075
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6385886
X-RAY DIFFRACTIONr_angle_other_deg0.4671.5569436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.633559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00610683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
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_it1.9632.2042275
X-RAY DIFFRACTIONr_mcbond_other1.9622.2042275
X-RAY DIFFRACTIONr_mcangle_it3.0333.292827
X-RAY DIFFRACTIONr_mcangle_other3.0333.292828
X-RAY DIFFRACTIONr_scbond_it2.6192.5962067
X-RAY DIFFRACTIONr_scbond_other2.6192.5962068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1333.7363059
X-RAY DIFFRACTIONr_long_range_B_refined5.86933.8574910
X-RAY DIFFRACTIONr_long_range_B_other5.8231.8524829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.997 Å
RfactorNum. reflection% reflection
Rfree0.285 77 -
Rwork0.218 1741 -
obs--55.28 %

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