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- PDB-7f0f: Crystal structure of capreomycin phosphotransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7f0f
TitleCrystal structure of capreomycin phosphotransferase in complex with CMN IIB
Components
  • Capreomycin phosphotransferase
  • DPP-ALA-DPP-UAL-MYN-KBE
KeywordsTRANSFERASE / Cph / phosphotransferase / capreomycin / resistance
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / ATP binding / Capreomycin 1B / Capreomycin phosphotransferase
Function and homology information
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChang, C.Y. / Pan, Y.C. / Wang, Y.L. / Toh, S.I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)107-2113-M-009-021-MY3 Taiwan
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Dual-Mechanism Confers Self-Resistance to the Antituberculosis Antibiotic Capreomycin.
Authors: Pan, Y.C. / Wang, Y.L. / Toh, S.I. / Hsu, N.S. / Lin, K.H. / Xu, Z. / Huang, S.C. / Wu, T.K. / Li, T.L. / Chang, C.Y.
History
DepositionJun 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capreomycin phosphotransferase
C: DPP-ALA-DPP-UAL-MYN-KBE


Theoretical massNumber of molelcules
Total (without water)32,1072
Polymers32,1072
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint0 kcal/mol
Surface area14340 Å2
Unit cell
Length a, b, c (Å)92.101, 92.101, 119.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Capreomycin phosphotransferase


Mass: 31436.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Gene: cph / Production host: Escherichia coli (E. coli) / References: UniProt: Q53826
#2: Protein/peptide DPP-ALA-DPP-UAL-MYN-KBE / CMN IIB


Type: Cyclic peptide / Class: Inhibitor / Mass: 670.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix mutabilis subsp. capreolus (bacteria)
Production host: Escherichia coli (E. coli) / References: Capreomycin 1B
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M sodium malonate pH 7.0, 0.1 M Bis-Tris propane pH 7.0, 0.1 M calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 30103 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.9764 / Net I/σ(I): 49.02
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.45 / Num. unique obs: 2918 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F0A

7f0a


Resolution: 2.1→21.15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.741 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2321 7.7 %RANDOM
Rwork0.1863 ---
obs0.1891 27774 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.22 Å2 / Biso mean: 31.763 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→21.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 46 199 2407
Biso mean--35.05 39.6 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172102
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.6442986
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5934815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10420.16125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90315328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8091524
X-RAY DIFFRACTIONr_chiral_restr0.1240.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022538
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02495
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 179 -
Rwork0.259 1965 -
all-2144 -
obs--97.81 %

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