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- PDB-4xu3: Mycobacterium tuberculosis biotin ligase complexed with bisubstra... -

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Basic information

Entry
Database: PDB / ID: 4xu3
TitleMycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 90 that has an acyclic ether in place of the ribose
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE/LIGASE INHIBITOR / biotin-protein ligase / bisubstrate inhibitor / LIGASE-LIGASE INHIBITOR COMPLEX
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] 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 / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. ...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 / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-44R / biotin--[biotin carboxyl-carrier protein] ligase / Biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24267703977 Å
AuthorsDe la Mora-Rey, T. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI091790-01 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors.
Authors: Bockman, M.R. / Kalinda, A.S. / Petrelli, R. / De la Mora-Rey, T. / Tiwari, D. / Liu, F. / Dawadi, S. / Nandakumar, M. / Rhee, K.Y. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C.
History
DepositionJan 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references / Experimental preparation
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1315
Polymers57,0692
Non-polymers1,0633
Water3,225179
1
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0833
Polymers28,5341
Non-polymers5492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0482
Polymers28,5341
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.326, 68.73, 114.093
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
DetailsThe biological unit is a monomer

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Components

#1: Protein Bifunctional ligase/repressor BirA / Biotin--acetyl-CoA-carboxylase ligase / Biotin-protein ligase / BirA protein


Mass: 28534.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_ ...Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_01710, IQ44_01750, IQ45_01765, IQ46_01705, IQ47_01735, IQ48_01770, IU12_01860, IU13_01785, IU14_01730, IU16_01770, IU17_01745, IU18_01730, IU19_01775, IU20_01750, IU22_01755, IU23_01750, IU24_01735, IZ84_17515, JE53_17495, LJ70_17695, T209_01770
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): MACH I
References: UniProt: A0A045H8W3, UniProt: I6YFP0*PLUS, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-44R / N-({2-[(6-amino-9H-purin-9-yl)methoxy]ethyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 513.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H27N9O5S2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17-24% PEG2000 MME, 100 mM Tris, pH 8.5, 100 mM triethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 13, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.243→50 Å / Num. obs: 23132 / % possible obs: 94.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.648400123 Å2 / Rsym value: 0.043 / Net I/σ(I): 12.3
Reflection shellResolution: 2.243→2.29 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 1.47 / % possible all: 84.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RUX

3rux


Resolution: 2.24267703977→31.663 Å / SU ML: 0.244237070459 / Cross valid method: FREE R-VALUE / σ(F): 1.38118602749 / Phase error: 23.0558163096
RfactorNum. reflection% reflection
Rfree0.232363977301 1198 5.18435173966 %
Rwork0.18541112631 21910 -
obs0.187883290453 23108 94.2183804942 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.0197844113 Å2
Refinement stepCycle: LAST / Resolution: 2.24267703977→31.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 69 179 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002087118611854053
X-RAY DIFFRACTIONf_angle_d0.7673820094255527
X-RAY DIFFRACTIONf_chiral_restr0.0263394677639648
X-RAY DIFFRACTIONf_plane_restr0.00312889421224728
X-RAY DIFFRACTIONf_dihedral_angle_d14.01546928131497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2427-2.33240.2818673615451200.2379499207922165X-RAY DIFFRACTION85.1658591129
2.3324-2.43860.2726418943931280.229716938262375X-RAY DIFFRACTION93.0829304574
2.4386-2.56710.2812138212681330.2218767858982321X-RAY DIFFRACTION92.4990576706
2.5671-2.72780.319273403581250.2244369522072372X-RAY DIFFRACTION92.3788383278
2.7278-2.93830.2589220819631270.2211846299192446X-RAY DIFFRACTION95.6505576208
2.9383-3.23370.2359011703191610.206031342052517X-RAY DIFFRACTION98.6735445836
3.2337-3.7010.2345771127021420.1864150407842551X-RAY DIFFRACTION98.4283625731
3.701-4.66050.2025979191411320.1548027816892563X-RAY DIFFRACTION97.503617945
4.6605-31.66610.1884535120971300.1507192055242600X-RAY DIFFRACTION94.3657103353

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