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- PDB-7f0c: Crystal structure of capreomycin phosphotransferase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7f0c
TitleCrystal structure of capreomycin phosphotransferase in complex with CMN IIA
Components
  • Capreomycin phosphotransferase
  • DPP-SER-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 IA / Capreomycin phosphotransferase
Function and homology information
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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-SER-DPP-UAL-MYN-KBE


Theoretical massNumber of molelcules
Total (without water)32,1232
Polymers32,1232
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint1 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.355, 92.355, 119.164
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-SER-DPP-UAL-MYN-KBE


Type: Cyclic peptide / Class: Inhibitor / Mass: 686.723 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 IA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.96 Å3/Da / Density % sol: 68.9 %
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: 2.07→30 Å / Num. obs: 32042 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.9765 / Net I/σ(I): 58.4
Reflection shellResolution: 2.07→2.14 Å / Mean I/σ(I) obs: 3.66 / Num. unique obs: 3156 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F0A

7f0a


Resolution: 2.07→25.06 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.978 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1585 4.9 %RANDOM
Rwork0.2174 ---
obs0.2191 30436 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.01 Å2 / Biso mean: 32.13 Å2 / Biso min: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0 Å2
2---0.19 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 2.07→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 9 131 2294
Biso mean--60.65 33.05 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132200
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172121
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6442987
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5964844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.90520.16125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97315329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1911524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022534
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02515
LS refinement shellResolution: 2.071→2.125 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 116 -
Rwork0.281 2174 -
all-2290 -
obs--99.01 %

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