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- PDB-7jt6: Mycobacterium tuberculosis dethiobiotin synthetase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7jt6
TitleMycobacterium tuberculosis dethiobiotin synthetase in complex with Tetrazole 2
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsLIGASE / inhibitor
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-VJG / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPederick, J.P. / Bean, J.H. / Bruning, J.B.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Inhibition of Mycobacterium tuberculosis Dethiobiotin Synthase ( Mt DTBS): Toward Next-Generation Antituberculosis Agents.
Authors: Schumann, N.C. / Lee, K.J. / Thompson, A.P. / Salaemae, W. / Pederick, J.L. / Avery, T. / Gaiser, B.I. / Hodgkinson-Bean, J. / Booker, G.W. / Polyak, S.W. / Bruning, J.B. / Wegener, K.L. / Abell, A.D.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,67322
Polymers93,1434
Non-polymers2,53018
Water6,125340
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,74010
Polymers46,5712
Non-polymers1,1698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-65 kcal/mol
Surface area17050 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,93312
Polymers46,5712
Non-polymers1,36110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-93 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.156, 104.178, 153.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ATP-dependent dethiobiotin synthetase BioD / DTB synthetase / DTBS / Dethiobiotin synthase


Mass: 23285.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: bioD, Rv1570, MTCY336.33c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase
#2: Chemical
ChemComp-VJG / {(1S,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}acetic acid


Mass: 300.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.7 M ammonium sulfate, 0.1 M Tris pH 8, 10-15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→49.33 Å / Num. obs: 59724 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Net I/σ(I): 18.2 / Num. measured all: 815941 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0514.21.5046184543480.8620.4131.561.9100
8.94-49.3312.60.021975377410.0060.02189.199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.66 Å49.33 Å
Translation6.66 Å49.33 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NMZ

6nmz


Resolution: 2→48.05 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2938 4.93 %
Rwork0.2142 56664 -
obs0.2152 59602 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.76 Å2 / Biso mean: 43.171 Å2 / Biso min: 31.55 Å2
Refinement stepCycle: final / Resolution: 2→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 162 340 6735
Biso mean--40.23 42.54 -
Num. residues----906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.030.39071260.341526592785
2.03-2.070.33071400.324326692809
2.07-2.110.29351260.311826562782
2.11-2.150.29151320.29926842816
2.15-2.190.28451490.279326302779
2.19-2.240.34631390.268226692808
2.24-2.290.27431470.249826482795
2.29-2.350.25631340.238226962830
2.35-2.410.27171340.240826512785
2.41-2.480.2771550.242126912846
2.48-2.560.25611410.229826612802
2.56-2.650.28871460.234426682814
2.65-2.760.2971490.240826732822
2.76-2.880.27361330.24727092842
2.88-3.040.27611220.239427072829
3.04-3.230.2671300.22827142844
3.23-3.480.22121410.214227272868
3.48-3.830.20841430.199127152858
3.83-4.380.18311390.164727542893
4.38-5.510.17081540.168927782932
5.52-48.050.20121580.184129053063

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