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- PDB-7jt5: Mycobacterium tuberculosis dethiobiotin synthetase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7jt5
TitleMycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 9
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsLIGASE/LIGASE INHIBITOR / inhibitor / LIGASE / LIGASE-LIGASE INHIBITOR complex
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-VJS / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPederick, J.P. / 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)95,90523
Polymers93,1434
Non-polymers2,76219
Water7,170398
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00112
Polymers46,5712
Non-polymers1,42910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-138 kcal/mol
Surface area16850 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,90411
Polymers46,5712
Non-polymers1,3339
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-95 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.648, 105.023, 152.719
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-VJS / {(1R,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}propanedioic acid


Mass: 334.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
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: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→49.17 Å / Num. obs: 61426 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Net I/σ(I): 16.4 / Num. measured all: 815221 / Scaling rejects: 40
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
2-2.0513.61.4926118144880.8280.4181.551.9100
8.94-49.1712.30.026984579910.0070.02767.299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.7 Å46.81 Å
Translation6.7 Å46.81 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→46.81 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 3023 4.93 %
Rwork0.2035 58267 -
obs0.205 61290 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.17 Å2 / Biso mean: 42.4613 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 2→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 175 398 6815
Biso mean--39.12 44.54 -
Num. residues----906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.030.32391470.291425912738
2.03-2.060.32691670.276925992766
2.06-2.10.30811510.266325762727
2.1-2.140.31191300.259926362766
2.14-2.180.30561470.256325792726
2.18-2.220.26841300.2426422772
2.22-2.270.24161290.238625922721
2.27-2.330.30421250.232626672792
2.33-2.380.26821420.220825922734
2.38-2.450.22421270.223526382765
2.45-2.520.26291450.216526382783
2.52-2.60.26861150.22926342749
2.6-2.690.29561260.23626602786
2.69-2.80.29421140.230926632777
2.8-2.930.24851220.232126632785
2.93-3.080.27241480.221726412789
3.08-3.280.24851540.219526532807
3.28-3.530.22271460.210626212767
3.53-3.880.25371400.191626722812
3.89-4.450.18041390.169126902829
4.45-5.60.18861560.168427392895
5.6-46.810.18491230.170928813004

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