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- PDB-9drk: Crystal structure of Mycobacterium tuberculosis biotin protein li... -

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Basic information

Entry
Database: PDB / ID: 9drk
TitleCrystal structure of Mycobacterium tuberculosis biotin protein ligase in complex with Bio-1
ComponentsBiotin--[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotin protein ligase / Adenylation inhibitors / Nucleoside
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / biotin binding / protein modification process / positive regulation of cell population proliferation / protein homodimerization activity / protein-containing complex / ATP binding / cytoplasm
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
: / Biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMcCue, W.M. / Jayasinghe, Y.P. / Aldrich, C.C. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI143784 United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Metabolically Stable Adenylation Inhibitors of Biotin Protein Ligase as Antibacterial Agents.
Authors: Liu, Q. / Engelhart, C.A. / Wallach, J.B. / Tiwari, D. / Ge, P. / Manna, A. / Panda, S. / McCue, W.M. / Wong, T.Y. / Sharma, S. / Jayasinghe, Y.P. / Fuller, J. / Ronning, D.R. / Bockman, M.R. ...Authors: Liu, Q. / Engelhart, C.A. / Wallach, J.B. / Tiwari, D. / Ge, P. / Manna, A. / Panda, S. / McCue, W.M. / Wong, T.Y. / Sharma, S. / Jayasinghe, Y.P. / Fuller, J. / Ronning, D.R. / Bockman, M.R. / Cheung, A. / Dartois, V. / Zimmerman, M.D. / Schnappinger, D. / Aldrich, C.C.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin--[acetyl-CoA-carboxylase] ligase
B: Biotin--[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1074
Polymers55,9922
Non-polymers1,1152
Water1,29772
1
A: Biotin--[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5532
Polymers27,9961
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Biotin--[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5532
Polymers27,9961
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.651, 68.705, 115.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--[biotin carboxyl-carrier protein] ligase / Biotin--protein ligase / BPL / Biotin-[acetyl- ...Biotin--[biotin carboxyl-carrier protein] ligase / Biotin--protein ligase / BPL / Biotin-[acetyl-CoA carboxylase] synthetase


Mass: 27995.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: birA, Rv3279c / Production host: Escherichia coli (E. coli)
References: UniProt: I6YFP0, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-A1BGE / 5'-deoxy-5'-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}sulfamamido)adenosine


Mass: 557.647 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31N9O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% MPEG 2000, 50 mM trimethylamine N-oxide, and 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→42.95 Å / Num. obs: 28673 / % possible obs: 94.03 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 12.23
Reflection shellResolution: 2.13→2.206 Å / Num. unique obs: 2784 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→42.95 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1353 5.02 %
Rwork0.1934 --
obs0.1968 26971 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 74 72 3945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093975
X-RAY DIFFRACTIONf_angle_d1.075443
X-RAY DIFFRACTIONf_dihedral_angle_d30.623593
X-RAY DIFFRACTIONf_chiral_restr0.063655
X-RAY DIFFRACTIONf_plane_restr0.006707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.20.32571380.24742656X-RAY DIFFRACTION99
2.2-2.290.30091120.23472065X-RAY DIFFRACTION77
2.29-2.390.29971290.21262691X-RAY DIFFRACTION99
2.39-2.520.28941550.20452670X-RAY DIFFRACTION100
2.52-2.640.2991900.22092050X-RAY DIFFRACTION98
2.69-2.890.31571350.21762458X-RAY DIFFRACTION100
2.89-3.180.30441600.20842691X-RAY DIFFRACTION100
3.18-3.630.27621430.19212731X-RAY DIFFRACTION100
3.63-4.580.21921390.16552730X-RAY DIFFRACTION99
4.58-42.950.22741520.18262876X-RAY DIFFRACTION99

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