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- PDB-5yk0: The complex structure of Rv3197-ADP from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5yk0
TitleThe complex structure of Rv3197-ADP 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 / ADENOSINE-5'-DIPHOSPHATE / Probable conserved ATP-binding protein ABC transporter
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 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)50,87911
Polymers49,5991
Non-polymers1,28010
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable conserved ATP-binding protein ABC transporter
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)305,27566
Polymers297,5966
Non-polymers7,67960
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area46300 Å2
ΔGint-599 kcal/mol
Surface area98520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.963, 186.963, 67.286
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0M lithium sulfate, 0.1M Tris (pH 8.5), 2% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 40630 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1974 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJZ

5yjz


Resolution: 2.102→45.273 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.84
RfactorNum. reflection% reflection
Rfree0.2283 2031 5.02 %
Rwork0.1908 --
obs0.1927 40423 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→45.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 75 342 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043229
X-RAY DIFFRACTIONf_angle_d0.8684377
X-RAY DIFFRACTIONf_dihedral_angle_d14.661222
X-RAY DIFFRACTIONf_chiral_restr0.031485
X-RAY DIFFRACTIONf_plane_restr0.004564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1022-2.15110.2421190.20952335X-RAY DIFFRACTION93
2.1511-2.20480.20321580.20632475X-RAY DIFFRACTION99
2.2048-2.26450.24451340.20792529X-RAY DIFFRACTION100
2.2645-2.33110.27441180.20972565X-RAY DIFFRACTION100
2.3311-2.40630.28091270.20762543X-RAY DIFFRACTION100
2.4063-2.49230.24551170.20232563X-RAY DIFFRACTION100
2.4923-2.59210.24521360.20242541X-RAY DIFFRACTION100
2.5921-2.71010.24551480.20762544X-RAY DIFFRACTION100
2.7101-2.85290.26081360.20552545X-RAY DIFFRACTION100
2.8529-3.03160.2241370.21182570X-RAY DIFFRACTION100
3.0316-3.26560.24411470.19392555X-RAY DIFFRACTION100
3.2656-3.59420.22981440.19022600X-RAY DIFFRACTION100
3.5942-4.11390.20821610.16142577X-RAY DIFFRACTION100
4.1139-5.18190.22431260.15952672X-RAY DIFFRACTION100
5.1819-45.28370.18221230.1952778X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -74.8595 Å / Origin y: 23.5845 Å / Origin z: 9.1689 Å
111213212223313233
T0.2601 Å2-0.0074 Å2-0.0708 Å2-0.1382 Å2-0.0771 Å2--0.217 Å2
L0.1194 °20.0422 °2-0.1503 °2-0.4549 °20.1209 °2--0.2577 °2
S-0.0393 Å °-0.0255 Å °0.0548 Å °0.0379 Å °0.0465 Å °-0.0281 Å °0.11 Å °0.0059 Å °0.0247 Å °
Refinement TLS groupSelection details: all

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