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- PDB-8eni: Crystal structure of Staphylococcus aureus biotin protein ligase ... -

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Basic information

Entry
Database: PDB / ID: 8eni
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE/LIGASE INHIBITOR / Biotin protein ligase / inhibitor / DNA BINDING PROTEIN / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / protein lipoylation / transferase activity / regulation of DNA-templated transcription / DNA binding / ATP binding
Similarity search - Function
Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-WNE / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWilce, M.C.J. / Cini, D.A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: ACS Infect Dis / Year: 2018
Title: Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus.
Authors: Paparella, A.S. / Lee, K.J. / Hayes, A.J. / Feng, J. / Feng, Z. / Cini, D. / Deshmukh, S. / Booker, G.W. / Wilce, M.C.J. / Polyak, S.W. / Abell, A.D.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5172
Polymers38,0151
Non-polymers5031
Water97354
1
A: Bifunctional ligase/repressor BirA
hetero molecules

A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0354
Polymers76,0302
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area2020 Å2
ΔGint-7 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.240, 94.240, 131.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

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


Mass: 38014.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: birA, SAV1456 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3JRH8, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-WNE / 3-[4-(5-fluoro-4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)butyl]-5-methyl-1,3-benzoxazol-2(3H)-one


Mass: 502.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31FN6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MOPS, MgCl,PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→47.13 Å / Num. obs: 22829 / % possible obs: 95.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 1.23
Reflection shellResolution: 2.4→2.48 Å / Num. unique obs: 8264 / CC1/2: 0.456

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20220110data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AQQ

6aqq


Resolution: 2.4→39.67 Å / SU ML: 0.3906 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2364 1139 5 %
Rwork0.2038 21662 -
obs0.2054 22801 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 35 54 2696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132695
X-RAY DIFFRACTIONf_angle_d1.35133635
X-RAY DIFFRACTIONf_chiral_restr0.0757393
X-RAY DIFFRACTIONf_plane_restr0.0106466
X-RAY DIFFRACTIONf_dihedral_angle_d17.5727997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.43691400.38482644X-RAY DIFFRACTION95.8
2.51-2.640.33581420.30972714X-RAY DIFFRACTION97.71
2.64-2.80.30881440.25762718X-RAY DIFFRACTION97.55
2.8-3.020.31231430.27042721X-RAY DIFFRACTION97.32
3.02-3.320.28111410.23242728X-RAY DIFFRACTION96.79
3.32-3.80.22281430.19482700X-RAY DIFFRACTION95.43
3.8-4.790.17621420.16362703X-RAY DIFFRACTION93.65
4.79-39.670.21251440.16932734X-RAY DIFFRACTION90.25
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.509356544792.57230241882-3.012342659944.36276902821-3.70896353754.258512720950.205925140898-0.0703267344528-0.02169037991750.159227475947-0.001465089062360.3089209447580.0430271957668-0.277680979846-0.160632676720.494997363155-0.0816953275079-0.1524075749750.4397295156460.05720448063410.43189358105928.252553595481.046073092737.5156482614
22.70171752221-0.4575220488920.4882361664762.26847913392-1.076562942283.637093012770.2054766361820.380547818357-0.189654567539-0.4088905304820.1137698305280.3494637899270.26008216191-0.545122298871-0.294118406540.548805732492-0.00283951259252-0.1290673035720.4231348724120.04089632510080.42083201385427.811159688991.475446847412.41721076
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 133 )2 - 1331 - 131
22chain 'A' and (resid 134 through 323 )134 - 323132 - 321

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