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- PDB-5yk2: The complex structure of Rv3197-erythromycin from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5yk2
TitleThe complex structure of Rv3197-erythromycin from Mycobacterium tuberculosis
ComponentsProbable conserved ATP-binding protein ABC transporter
KeywordsTRANSPORT PROTEIN / Mycobacterium tuberculosis / macrolide antibiotic binding protein / non-canonical ABC protein
Function / homologyABC1 atypical kinase-like domain / ADCK3-like domain / : / ABC1 atypical kinase-like domain / peptidoglycan-based cell wall / Protein kinase-like domain superfamily / ATP binding / ERYTHROMYCIN A / Probable conserved ATP-binding protein ABC transporter
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.807 Å
AuthorsRao, Z.H. / Zhang, Q.Q.
Funding support China, 3items
OrganizationGrant numberCountry
State Key Development Program for Basic Research of the Ministry of Science and Technology of China2014CB542800 China
National Natural Science Foundation of China81330036 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Protein Cell / Year: 2018
Title: Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target.
Authors: Zhang, Q. / Liu, H. / Liu, X. / Jiang, D. / Zhang, B. / Tian, H. / Yang, C. / Guddat, L.W. / Yang, H. / Mi, K. / Rao, Z.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable conserved ATP-binding protein ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3332
Polymers49,5991
Non-polymers7341
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-7 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.238, 187.238, 67.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Probable conserved ATP-binding protein ABC transporter / macrolide antibiotic binding protein


Mass: 49599.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3197 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3) RIL / References: UniProt: O53343
#2: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM

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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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1M Bis-Tris (pH 6.5), 2% (v/v) polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17350 / % possible obs: 99.4 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 26.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1686 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJZ

5yjz


Resolution: 2.807→34.712 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2738 886 5.19 %
Rwork0.2294 --
obs0.2317 17071 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.807→34.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 51 0 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023157
X-RAY DIFFRACTIONf_angle_d0.7214284
X-RAY DIFFRACTIONf_dihedral_angle_d12.8611219
X-RAY DIFFRACTIONf_chiral_restr0.025490
X-RAY DIFFRACTIONf_plane_restr0.004553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8072-2.9830.33461540.29852442X-RAY DIFFRACTION92
2.983-3.21310.32791510.27482694X-RAY DIFFRACTION99
3.2131-3.53620.28481500.25782712X-RAY DIFFRACTION100
3.5362-4.04720.27461570.2222713X-RAY DIFFRACTION100
4.0472-5.09650.21991410.20142771X-RAY DIFFRACTION99
5.0965-34.71470.27111330.20892853X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -74.8865 Å / Origin y: 23.6794 Å / Origin z: 9.7816 Å
111213212223313233
T0.5257 Å2-0.009 Å2-0.1726 Å2-0.3796 Å2-0.3295 Å2--0.502 Å2
L0.2303 °20.0895 °2-0.0971 °2-0.5451 °20.2364 °2--0.3158 °2
S-0.1275 Å °-0.0376 Å °0.0751 Å °0.0507 Å °0.186 Å °-0.0987 Å °0.2257 Å °0.1199 Å °0.0317 Å °
Refinement TLS groupSelection details: all

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