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- PDB-8f8u: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae (Do... -

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Basic information

Entry
Database: PDB / ID: 8f8u
TitleBifunctional ligase/repressor BirA from Klebsiella pneumoniae (Domain Swapped Dimer)
ComponentsBifunctional ligase/repressor BirA
KeywordsTRANSCRIPTION / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Biotin operon repressor, helix-turn-helix domain / 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 ...Biotin operon repressor, helix-turn-helix domain / 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
IMIDAZOLE / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae (Domain Swapped Dimer)
Authors: Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)73,1444
Polymers73,0062
Non-polymers1382
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-18 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.910, 155.740, 58.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 36502.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)
Gene: birA, B4U61_27335, B5L96_27980, BL124_00027250, BN49_4485, DDJ63_29720, DRB11_28835, EAO17_15035, FXN67_30565, G7Z27_25945, GJJ08_025595, GNE24_27625, GNG14_18750, HV479_27705, NCTC11679_05451, ...Gene: birA, B4U61_27335, B5L96_27980, BL124_00027250, BN49_4485, DDJ63_29720, DRB11_28835, EAO17_15035, FXN67_30565, G7Z27_25945, GJJ08_025595, GNE24_27625, GNG14_18750, HV479_27705, NCTC11679_05451, NCTC204_01612, NCTC3279_04746, NCTC5047_03297, NCTC5052_03568, NCTC8849_00281, NCTC9140_00986, NCTC9637_06311, NCTC9645_02159, NCTC9661_00981, SAMEA3499874_05300, SAMEA3499901_05308, SAMEA3500057_05333, SAMEA3512100_05201, SAMEA3538828_05246, SAMEA3649758_05372, SAMEA3720909_05478, SAMEA3727643_05796, SAMEA3727679_05497, SAMEA4364603_05401
Plasmid: Klpnc.17896.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0W7ZMT5, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus G3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate ...Details: Morpheus G3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate, KlpnC.17896.a.B1.PW39036 at 30 mg/mL. Tray: Clover-Liu-S-045 / B1 , Puck: CPS5110_06, Cryo: 150% Morpheus G3. Protein crystals were dehydrated in this solution for 3 days before freezing.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 30, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→84.093 Å / Num. obs: 20235 / % possible obs: 94.2 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.1
Reflection shellResolution: 2.85→2.98 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.709 / Mean I/σ(I) obs: 1 / Num. unique obs: 1012 / CC1/2: 0.427 / % possible all: 49.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→29.74 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1001 4.96 %
Rwork0.2147 --
obs0.2167 20186 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 10 2 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054629
X-RAY DIFFRACTIONf_angle_d0.7886282
X-RAY DIFFRACTIONf_dihedral_angle_d18.5331678
X-RAY DIFFRACTIONf_chiral_restr0.055731
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.4054640.35351238X-RAY DIFFRACTION42
3-3.190.37861470.33592839X-RAY DIFFRACTION97
3.19-3.430.34791450.28282986X-RAY DIFFRACTION100
3.43-3.780.30661610.24432954X-RAY DIFFRACTION100
3.78-4.320.26751680.21712988X-RAY DIFFRACTION100
4.32-5.440.24751460.18463038X-RAY DIFFRACTION100
5.44-29.740.20351700.1933142X-RAY DIFFRACTION99
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)
16.09352.15983.06153.77012.23092.97980.1524-0.5297-0.67410.1728-0.33520.75340.1499-0.67160.15790.69190.0320.13270.94250.02790.71547.679716.319533.5975
23.3052-0.18761.36557.7109-1.82023.80340.33430.19160.09670.0684-0.20370.1666-0.25710.0823-0.12440.47270.0560.06480.55020.03420.222738.884127.260249.3296
34.5164-0.70342.28384.2145-0.13662.2343-0.0075-0.0454-0.01050.417-0.0823-0.77270.1460.30960.13750.6467-0.03570.01580.65240.03730.401149.090625.253254.0056
41.24881.5596-0.0363.75250.51080.1516-0.20790.20070.5607-0.14590.29290.1051-0.51560.1998-0.05211.07570.0358-0.05630.90160.07860.996129.683446.94734.5347
53.3386-0.3062-1.62393.34631.49793.7634-0.1890.2325-0.4492-0.1489-0.17680.0455-0.00730.3420.38660.48870.0208-0.00470.64010.12750.387530.80887.308715.2031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 317 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 317 )

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