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- PDB-7f0a: Crystal structure of capreomycin phosphotransferase -

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Basic information

Entry
Database: PDB / ID: 7f0a
TitleCrystal structure of capreomycin phosphotransferase
ComponentsCapreomycin phosphotransferase
KeywordsTRANSFERASE / Cph / phosphotransferase / capreomycin / resistance
Function / homology
Function and homology information


transferase activity / ATP binding
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Capreomycin phosphotransferase
Similarity search - Component
Biological speciesSaccharothrix mutabilis subsp. capreolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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


Theoretical massNumber of molelcules
Total (without water)31,4361
Polymers31,4361
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.969, 91.969, 120.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 4.04 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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 315r / Detector: CCD / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 37001 / % possible obs: 96.9 % / Redundancy: 9.9 % / CC1/2: 0.995 / Net I/σ(I): 50.6
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 3.56 / Num. unique obs: 3683 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGI

5igi


Resolution: 1.95→28.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.825 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1795 4.9 %RANDOM
Rwork0.1903 ---
obs0.1917 35206 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 42.332 Å2 / Biso min: 21.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.95→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 0 163 2279
Biso mean---50.92 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132156
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172058
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6322935
X-RAY DIFFRACTIONr_angle_other_deg1.5041.5784717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18620.325123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.011524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
LS refinement shellResolution: 1.951→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 157 -
Rwork0.269 2566 -
all-2723 -
obs--98.3 %

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