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- PDB-4xu1: Mycobacterium tuberculosis biotin ligase complexed with bisubstra... -

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Basic information

Entry
Database: PDB / ID: 4xu1
TitleMycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 82 that incorporates a morpholine 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--[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 / 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-44O / 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: 1.70001332019 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
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _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

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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)58,3987
Polymers57,0692
Non-polymers1,3305
Water11,782654
1
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2304
Polymers28,5341
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1683
Polymers28,5341
Non-polymers6342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.219, 71.38, 113.702
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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-44O / [(2S,6R)-6-(6-amino-9H-purin-9-yl)morpholin-2-yl]methyl {5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamate


Mass: 555.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N9O6S2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
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: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 57349 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.7212355927 Å2 / Rsym value: 0.08 / Net I/σ(I): 24.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.3 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RUX

3rux


Resolution: 1.70001332019→30.4545496915 Å / SU ML: 0.174664104094 / Cross valid method: FREE R-VALUE / σ(F): 1.34291264033 / Phase error: 19.7432895786
RfactorNum. reflection% reflection
Rfree0.202833678583 2905 5.07202095155 %
Rwork0.170925362526 54370 -
obs0.172563817399 57275 99.9441603993 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.3142597872 Å2
Refinement stepCycle: LAST / Resolution: 1.70001332019→30.4545496915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 86 654 4653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007389332740794093
X-RAY DIFFRACTIONf_angle_d1.308739716645594
X-RAY DIFFRACTIONf_chiral_restr0.0492712389843658
X-RAY DIFFRACTIONf_plane_restr0.00532112430142736
X-RAY DIFFRACTIONf_dihedral_angle_d16.58681816351521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72790.2530518046221130.2022221218832538X-RAY DIFFRACTION99.2512167727
1.7279-1.75770.262474995631220.1926465868822576X-RAY DIFFRACTION100
1.7577-1.78960.238923591711620.19798352342545X-RAY DIFFRACTION100
1.7896-1.8240.2422214988171150.189103185972549X-RAY DIFFRACTION100
1.824-1.86130.2424393783461210.1844287752392605X-RAY DIFFRACTION100
1.8613-1.90170.2175055258741640.1778997032582505X-RAY DIFFRACTION100
1.9017-1.9460.218175279791540.1830563018882548X-RAY DIFFRACTION99.9630040696
1.946-1.99460.2230378916011370.1898919250142567X-RAY DIFFRACTION100
1.9946-2.04850.2229371722791350.1828843788732565X-RAY DIFFRACTION100
2.0485-2.10880.2257485753181390.1803903149952592X-RAY DIFFRACTION99.9633967789
2.1088-2.17690.2299570718871430.1714514729182547X-RAY DIFFRACTION100
2.1769-2.25460.2134529239521190.1743546145362588X-RAY DIFFRACTION100
2.2546-2.34490.2186134523311620.1767887373842555X-RAY DIFFRACTION100
2.3449-2.45160.2083592606891330.1791863486942603X-RAY DIFFRACTION100
2.4516-2.58070.194666908391370.174487103482582X-RAY DIFFRACTION100
2.5807-2.74230.2402054509981360.1825109326222621X-RAY DIFFRACTION100
2.7423-2.95390.1997607301571420.1789403257252578X-RAY DIFFRACTION99.9632488056
2.9539-3.25090.2130560111381300.1781163857192635X-RAY DIFFRACTION100
3.2509-3.72060.1734738572981780.1578287254432604X-RAY DIFFRACTION100
3.7206-4.68480.1613380238531300.1372870070022664X-RAY DIFFRACTION100
4.6848-30.45940.1761663336341330.1628217281152803X-RAY DIFFRACTION99.6943972835

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