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- PDB-4xu2: Mycobacterium tuberculosis biotin ligase complexed with bisubstra... -

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Basic information

Entry
Database: PDB / ID: 4xu2
TitleMycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 87 with a 3'deoxy 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-44Q / 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: 1.85002844216 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)58,1804
Polymers57,0692
Non-polymers1,1112
Water9,206511
1
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0902
Polymers28,5341
Non-polymers5561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0902
Polymers28,5341
Non-polymers5561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.753, 68.875, 115.609
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-44Q / 3',5'-dideoxy-5'-[({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}sulfamoyl)amino]adenosine


Mass: 555.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N9O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
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: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→115.61 Å / Num. obs: 44260 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.2388518081 Å2 / Rsym value: 0.055 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.856 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8

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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
Resolution: 1.85002844216→36.3668016401 Å / SU ML: 0.198193004874 / Cross valid method: FREE R-VALUE / σ(F): 1.35504501685 / Phase error: 21.6073895711
RfactorNum. reflection% reflection
Rfree0.221926957374 2227 5.03948767849 %
Rwork0.190296030949 41964 -
obs0.191909591558 44191 99.932158929 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.5055983662 Å2
Refinement stepCycle: LAST / Resolution: 1.85002844216→36.3668016401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 74 511 4466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001923767757474042
X-RAY DIFFRACTIONf_angle_d0.797236645525520
X-RAY DIFFRACTIONf_chiral_restr0.0261050901598649
X-RAY DIFFRACTIONf_plane_restr0.00328254683136724
X-RAY DIFFRACTIONf_dihedral_angle_d13.29816643791503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89030.2439247236711220.2191579110042607X-RAY DIFFRACTION100
1.8903-1.93420.2694776744131310.2211736814572616X-RAY DIFFRACTION100
1.9342-1.98260.2789524383621420.2161579342252555X-RAY DIFFRACTION100
1.9826-2.03620.2472834772231470.2169464595192600X-RAY DIFFRACTION99.9636098981
2.0362-2.09610.2986140397731400.2205076258732589X-RAY DIFFRACTION99.9633699634
2.0961-2.16370.2673219634131240.2176464551682601X-RAY DIFFRACTION100
2.1637-2.24110.2556637186521410.2082581439712567X-RAY DIFFRACTION100
2.2411-2.33080.2494439794881340.2088894921372619X-RAY DIFFRACTION99.9636891794
2.3308-2.43680.2455354915951410.2124606803222590X-RAY DIFFRACTION99.9633967789
2.4368-2.56530.2346587015421410.2074627110682617X-RAY DIFFRACTION99.8551774077
2.5653-2.7260.2503219024641320.213033428392622X-RAY DIFFRACTION99.9637023593
2.726-2.93630.2338571470661370.2040617229792630X-RAY DIFFRACTION99.8196248196
2.9363-3.23170.2172472635841670.1881326609142608X-RAY DIFFRACTION99.9639769452
3.2317-3.69890.2076994445931440.1724675652432638X-RAY DIFFRACTION99.8922800718
3.6989-4.65870.174883660951410.1526927495872695X-RAY DIFFRACTION99.8943289891
4.6587-36.37380.1827879367321430.1679305820752810X-RAY DIFFRACTION99.6961512492

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