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

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Basic information

Entry
Database: PDB / ID: 4xtv
TitleMycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 36 (N-({[(1R,3S)-3-(6-amino-9H-purin-9-yl)cyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide)
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-44K / 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: 1.45000836498 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 / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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)58,1444
Polymers57,0692
Non-polymers1,0752
Water11,476637
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A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0722
Polymers28,5341
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0722
Polymers28,5341
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.896, 68.937, 115.713
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

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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-44K / N-({[(1R,3S)-3-(6-amino-9H-purin-9-yl)cyclopentyl]methyl}sulfamoyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 537.659 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N9O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
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: Jul 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→36.415 Å / Num. obs: 91151 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.0042860797 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.8
Reflection shellResolution: 1.45→1.455 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RUX

3rux


Resolution: 1.45000836498→36.4153988479 Å / SU ML: 0.134117131829 / Cross valid method: FREE R-VALUE / σ(F): 1.35409701173 / Phase error: 20.2915302237
RfactorNum. reflection% reflection
Rfree0.205571552822 4562 5.00988359324 %
Rwork0.186154417257 86498 -
obs0.18715566626 91060 99.8694874916 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.8442553982 Å2
Refinement stepCycle: LAST / Resolution: 1.45000836498→36.4153988479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 72 637 4624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002795313819674202
X-RAY DIFFRACTIONf_angle_d0.9764168243525765
X-RAY DIFFRACTIONf_chiral_restr0.0537843425599674
X-RAY DIFFRACTIONf_plane_restr0.00421904691995767
X-RAY DIFFRACTIONf_dihedral_angle_d14.92753798381603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.2745302094321640.2349763773642843X-RAY DIFFRACTION100
1.4665-1.48370.2581880143141380.2204176867382854X-RAY DIFFRACTION100
1.4837-1.50180.252463633091450.2206954619332869X-RAY DIFFRACTION100
1.5018-1.52080.2561278573721300.2141218874122870X-RAY DIFFRACTION99.9666777741
1.5208-1.54090.2442410986391540.2144808422672850X-RAY DIFFRACTION100
1.5409-1.5620.2180085217661450.2121923179632863X-RAY DIFFRACTION100
1.562-1.58430.2445552243031390.2061924857962853X-RAY DIFFRACTION100
1.5843-1.60790.2410193498551520.2094008040862840X-RAY DIFFRACTION99.966588707
1.6079-1.63310.1999971281131420.2067973357472895X-RAY DIFFRACTION99.9670836076
1.6331-1.65980.2445077914151580.2051558969122829X-RAY DIFFRACTION99.9665327979
1.6598-1.68840.2695432388371550.2061215251252883X-RAY DIFFRACTION99.967094439
1.6884-1.71920.2452853928111380.2059807876862852X-RAY DIFFRACTION100
1.7192-1.75220.1989154031511520.2006858397092870X-RAY DIFFRACTION99.9008264463
1.7522-1.7880.2284530165311370.2043196495182875X-RAY DIFFRACTION99.8673740053
1.788-1.82690.219933983461530.2066369962872855X-RAY DIFFRACTION100
1.8269-1.86940.2492342561291640.2058234349612857X-RAY DIFFRACTION99.7688243065
1.8694-1.91610.2114807208311680.1961895606322876X-RAY DIFFRACTION99.9015425008
1.9161-1.96790.1995020605841540.1917407256992852X-RAY DIFFRACTION99.8671096346
1.9679-2.02580.2124436694281520.1886025779712851X-RAY DIFFRACTION99.8669770535
2.0258-2.09120.2065535118041680.1946122804122865X-RAY DIFFRACTION99.9341021417
2.0912-2.16590.2188759044191350.1897883352916X-RAY DIFFRACTION99.8363874346
2.1659-2.25260.2161500098281570.1869727363422863X-RAY DIFFRACTION99.6370834708
2.2526-2.35510.1940056196911460.1897953865092908X-RAY DIFFRACTION99.8365478915
2.3551-2.47930.1945136509141510.1884401717392885X-RAY DIFFRACTION99.8027613412
2.4793-2.63460.2229616929331600.1887136397882900X-RAY DIFFRACTION99.7717639387
2.6346-2.83790.2015364625551470.1944854665222901X-RAY DIFFRACTION99.8362266623
2.8379-3.12340.2038716922791690.1831548894762919X-RAY DIFFRACTION99.6450467893
3.1234-3.5750.1929634832071720.1666448392072913X-RAY DIFFRACTION99.5161290323
3.575-4.50280.1715945550031580.1560262343822976X-RAY DIFFRACTION99.7136493796
4.5028-36.42690.1810988062411590.1699871832563115X-RAY DIFFRACTION99.6651445967

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