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- PDB-6ndl: Crystal structure of Staphylococcus aureus biotin protein ligase ... -

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Basic information

Entry
Database: PDB / ID: 6ndl
TitleCrystal structure of Staphylococcus aureus biotin protein ligase in complex with a sulfonamide inhibitor
ComponentsBiotin Protein Ligase
KeywordsLIGASE/LIGASE INHIBITOR / BPL inhibitor / sulfonamide analogue / amino sulfonylurea / antibiotic / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / transferase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal 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 ...Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal 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 / 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) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BQX / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMarshall, A.C. / Polyak, S.W. / Bruning, J.B. / Lee, K.
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Sulfonamide-Based Inhibitors of Biotin Protein Ligase as New Antibiotic Leads.
Authors: Lee, K.J. / Tieu, W. / Blanco-Rodriguez, B. / Paparella, A.S. / Yu, J. / Hayes, A. / Feng, J. / Marshall, A.C. / Noll, B. / Milne, R. / Cini, D. / Wilce, M.C.J. / Booker, G.W. / Bruning, J.B. ...Authors: Lee, K.J. / Tieu, W. / Blanco-Rodriguez, B. / Paparella, A.S. / Yu, J. / Hayes, A. / Feng, J. / Marshall, A.C. / Noll, B. / Milne, R. / Cini, D. / Wilce, M.C.J. / Booker, G.W. / Bruning, J.B. / Polyak, S.W. / Abell, A.D.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 11, 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: Biotin Protein Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0597
Polymers38,0721
Non-polymers9876
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, Biological dimer is formed with symmetry-mate
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.031, 94.031, 130.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

21A-961-

HOH

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Components

#1: Protein Biotin Protein Ligase


Mass: 38071.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q2G258*PLUS, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BQX / 1-[4-(6-aminopurin-9-yl)butylsulfamoyl]-3-[4-[(4~{S})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butyl]urea


Mass: 526.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30N10O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.8 Å3/Da / Density % sol: 67.65 % / Description: square rod
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 14% PEG8000, 0.1M Tris pH 8.5, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2018
Details: Ce-/Nd-doped Yttrium Aluminium Garnet (YAG) crystal
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→46.66 Å / Num. obs: 40406 / % possible obs: 100 % / Redundancy: 28.4 % / Biso Wilson estimate: 52.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.025 / Rrim(I) all: 0.131 / Net I/σ(I): 16.1 / Num. measured all: 1149362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0529.56.7298617329190.2041.2446.8440.7100
8.94-46.6621.70.0361166753710.0070.03661.398.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.57 Å46.66 Å
Translation6.57 Å46.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6APW

6apw


Resolution: 2→46.657 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2028 5.03 %
Rwork0.1699 38312 -
obs0.1726 40340 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.47 Å2 / Biso mean: 71.2871 Å2 / Biso min: 32.26 Å2
Refinement stepCycle: final / Resolution: 2→46.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 100 464 3174
Biso mean--76.59 85.98 -
Num. residues----323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05010.37571420.363726882830100
2.0501-2.10550.39481250.343826832808100
2.1055-2.16750.31661530.295526812834100
2.1675-2.23740.32521460.279627012847100
2.2374-2.31740.31251540.259626782832100
2.3174-2.41020.28871500.231727052855100
2.4102-2.51990.28461550.209127052860100
2.5199-2.65270.24711220.190627252847100
2.6527-2.81890.24291390.185327302869100
2.8189-3.03650.2351120.188627692881100
3.0365-3.3420.21711580.163327412899100
3.342-3.82540.22171510.149227572908100
3.8254-4.81880.18531540.129327962950100
4.8188-46.670.19831670.15732953312099
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)
16.678-0.776-3.80425.9632.87037.70940.155-0.22610.4307-0.05630.0997-0.459-0.0874-0.167-0.23420.53550.18240.08240.63550.11390.526124.628924.459746.3907
22.56290.4137-0.49244.8954-0.13493.60330.05760.1170.38630.02950.22960.2082-0.5447-0.1616-0.28610.32610.02740.04710.46610.08610.381342.387417.627922.2486
33.72560.6918-1.55253.7387-0.29677.3718-0.00160.64650.4882-0.5690.36030.6747-0.6468-0.8455-0.35750.50560.0299-0.0530.60730.20.544539.081118.369410.1123
42.57332.7436-4.31848.5338-2.68068.7303-0.14420.5831-0.0558-0.60850.2499-0.5510.05520.2153-0.04620.7408-0.15240.10440.8117-0.01020.47752.727716.4037-0.7987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 62 )A2 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 240 )A63 - 240
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 288 )A241 - 288
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 324 )A289 - 324

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