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- PDB-7l1j: Mycobacterium tuberculosis dethiobiotin synthetase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7l1j
TitleMycobacterium tuberculosis dethiobiotin synthetase in complex with Tetrazole 1
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-XES / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsPederick, J.L. / 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
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Oct 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)95,46518
Polymers93,1434
Non-polymers2,32214
Water16,376909
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6368
Polymers46,5712
Non-polymers1,0656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-55 kcal/mol
Surface area17130 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82810
Polymers46,5712
Non-polymers1,2578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-59 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.866, 104.406, 153.787
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-XES / {(1R,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}propanedioic acid


Mass: 344.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16N4O5 / 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.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
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: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→38.45 Å / Num. obs: 117277 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 19.8 / Num. measured all: 1591319
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
1.6-1.6313.81.977906257150.6840.5452.0451.6100
8.76-38.4512.30.0191031883710.0050.0288.699

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.91 Å38.45 Å
Translation6.91 Å38.45 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NMZ

6nmz


Resolution: 1.6→38.45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 5940 5.07 %
Rwork0.1783 111218 -
obs0.1798 117158 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.2 Å2 / Biso mean: 29.1887 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 1.6→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 154 909 7339
Biso mean--25.52 38.56 -
Num. residues----908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.620.33441940.28836713865
1.62-1.640.30111940.280836353829
1.64-1.660.28471820.274537143896
1.66-1.680.29731990.253336053804
1.68-1.70.27592070.243637013908
1.7-1.720.25431970.243936373834
1.72-1.750.29311590.232336913850
1.75-1.770.2711890.225337133902
1.77-1.80.24551980.211336453843
1.8-1.830.26912160.211236913907
1.83-1.860.24721920.20336453837
1.86-1.90.21361930.189337263919
1.9-1.930.22732070.185836273834
1.93-1.970.24671980.189536843882
1.97-2.020.22891820.188936823864
2.02-2.060.23732050.18236813886
2.06-2.110.20441950.175637113906
2.11-2.170.20642130.173536523865
2.17-2.240.20271980.174137043902
2.24-2.310.19561950.17237033898
2.31-2.390.22242270.171336943921
2.39-2.490.2071920.180737203912
2.49-2.60.21311780.176137273905
2.6-2.740.21471830.183737613944
2.74-2.910.24972170.181737073924
2.91-3.130.20032100.180237103920
3.13-3.450.19122070.171437703977
3.45-3.940.20362060.163937833989
3.94-4.970.16051820.146638604042
4.97-38.450.17452250.168839684193

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