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- PDB-6bs5: Crystal structure of AMP-PNP-bound bacterial Get3-like A and B in... -

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Basic information

Entry
Database: PDB / ID: 6bs5
TitleCrystal structure of AMP-PNP-bound bacterial Get3-like A and B in Mycobacterium tuberculosis
Components
  • Anion transporter
  • Putative ATPase Rv3679
KeywordsUNKNOWN FUNCTION / Complex
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Probable anion transporter ATPase / ATPase BagA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLi, H. / Hu, K. / Kovach, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Bacteriol. / Year: 2019
Title: Characterization of Guided Entry of Tail-Anchored Proteins 3 Homologues in Mycobacterium tuberculosis.
Authors: Hu, K. / Jordan, A.T. / Zhang, S. / Dhabaria, A. / Kovach, A. / Rangel, M.V. / Ueberheide, B. / Li, H. / Darwin, K.H.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Putative ATPase Rv3679
B: Anion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9424
Polymers78,4122
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-45 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.129, 121.129, 120.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative ATPase Rv3679


Mass: 35893.141 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: Rv3679, MTV025.027 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKX5
#2: Protein Anion transporter


Mass: 42518.656 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: Rv3680 / Production host: Escherichia coli (E. coli) / References: UniProt: I6Y498
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG8000, calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.05969 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 20, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05969 Å / Relative weight: 1
ReflectionResolution: 3.1→28.282 Å / Num. obs: 18969 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.243 / Net I/σ(I): 8.2
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.958 / Num. unique obs: 2594

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BS3

6bs3


Resolution: 3.1→28.282 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.46
RfactorNum. reflection% reflection
Rfree0.2502 964 5.12 %
Rwork0.2148 --
obs0.2165 18832 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→28.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 32 0 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125262
X-RAY DIFFRACTIONf_angle_d1.3217150
X-RAY DIFFRACTIONf_dihedral_angle_d15.2583219
X-RAY DIFFRACTIONf_chiral_restr0.071865
X-RAY DIFFRACTIONf_plane_restr0.011924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26320.29481480.27862521X-RAY DIFFRACTION100
3.2632-3.46740.27991410.23892511X-RAY DIFFRACTION100
3.4674-3.73450.2861240.23292543X-RAY DIFFRACTION100
3.7345-4.10930.23271340.21642556X-RAY DIFFRACTION100
4.1093-4.70160.22931220.19142571X-RAY DIFFRACTION100
4.7016-5.91460.24291510.2152580X-RAY DIFFRACTION100
5.9146-28.28330.23281440.18942586X-RAY DIFFRACTION97

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