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- PDB-6oru: Crystal structure of Bira from S. aureus in complex with a acylsu... -

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Basic information

Entry
Database: PDB / ID: 6oru
TitleCrystal structure of Bira from S. aureus in complex with a acylsulfamide analogue of biotinyl-5'-AMP
ComponentsBifunctional ligase/repressor BirA
KeywordsLIGASE/INHIBITOR / biotin'-5'-analogue inhibitor / 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
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 / 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-N3G / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å
AuthorsWilce, M.C.J. / Cini, D.
CitationJournal: To Be Published
Title: Enhancing the stability of the sulfonamide linker of BPL inhibitors
Authors: Lee, K.J. / Abell, A.D.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5262
Polymers38,0151
Non-polymers5121
Water70339
1
A: Bifunctional ligase/repressor BirA
hetero molecules

A: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0534
Polymers76,0302
Non-polymers1,0232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1870 Å2
ΔGint-3 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.540, 92.540, 128.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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 (bacteria) / Gene: birA, M1K003_0300 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3A5LBF0, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-N3G / N-{[4-(6-amino-9H-purin-9-yl)butyl]sulfamoyl}-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 511.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N9O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 8000, 0.1 M 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: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→45.932 Å / Num. obs: 22803 / % possible obs: 99.94 % / Redundancy: 2 % / Net I/σ(I): 15.65
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 5001

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6apw

6apw


Resolution: 2.392→45.932 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1172 5.14 %RANDOM
Rwork0.1871 ---
obs0.1893 22800 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.392→45.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 34 39 2662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082676
X-RAY DIFFRACTIONf_angle_d0.8733616
X-RAY DIFFRACTIONf_dihedral_angle_d9.4141588
X-RAY DIFFRACTIONf_chiral_restr0.054394
X-RAY DIFFRACTIONf_plane_restr0.005465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3921-2.50090.40461210.30022665X-RAY DIFFRACTION100
2.5009-2.63280.31221380.26812657X-RAY DIFFRACTION100
2.6328-2.79770.28081590.24672643X-RAY DIFFRACTION100
2.7977-3.01370.27421300.21982683X-RAY DIFFRACTION100
3.0137-3.31690.2431560.19662668X-RAY DIFFRACTION100
3.3169-3.79660.2151560.17322688X-RAY DIFFRACTION100
3.7966-4.78250.18971480.15062742X-RAY DIFFRACTION100
4.7825-45.94050.20831640.17752882X-RAY DIFFRACTION100
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)
15.2431-1.3157-0.90414.13231.0015.211-0.2039-0.73490.19840.13770.3773-0.560.0710.1683-0.17340.40680.17120.10090.61360.06480.448924.228324.191546.3187
22.7176-0.6089-1.78413.86412.29013.7321-0.041-0.43150.1410.5950.2190.25550.1350.1644-0.1070.4140.05860.10570.66190.04450.480234.259815.487832.8265
31.62030.5283-1.12784.66740.01433.0714-0.1184-0.33850.0630.25640.3752-0.1679-0.2112-0.0355-0.27780.2701-0.00270.05150.496-0.02320.43344.298411.776625.4455
41.9563-0.3812-0.51234.7621.87363.0621-0.03820.19710.1737-0.49160.22050.2345-0.4262-0.1959-0.17610.5706-0.01680.1050.60360.19480.544839.750621.523511.7929
52.63721.3594-0.07644.13221.19492.58010.12280.00860.408-0.00370.24230.0914-0.6107-0.1923-0.34740.4001-0.0080.12650.45590.06770.440840.539720.527120.2565
64.9546-0.6237-1.12743.2844-0.97264.08810.52291.19770.7263-0.59540.0203-0.1569-0.5258-0.2143-0.44370.8396-0.10050.12780.62980.08140.429844.445119.76522.6334
72.58430.0843-0.44663.2899-0.64723.3223-0.0421-0.01430.1949-0.6327-0.1166-0.4827-0.06810.17370.11170.7353-0.16370.21810.65150.03020.528651.151916.5506-1.18
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 261 )
6X-RAY DIFFRACTION6chain 'A' and (resid 262 through 288 )
7X-RAY DIFFRACTION7chain 'A' and (resid 289 through 323 )

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