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- PDB-8fi3: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae com... -

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Basic information

Entry
Database: PDB / ID: 8fi3
TitleBifunctional ligase/repressor BirA from Klebsiella pneumoniae complexed with biotin (Domain Swapped Dimer)
ComponentsBifunctional ligase/repressor BirA
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / regulation of DNA-templated transcription / DNA binding / ATP binding
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 / 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
BIOTIN / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 DirectorS10OD030394 United States
CitationJournal: To be published
Title: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae complexed with biotin (Domain Swapped Dimer)
Authors: Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 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)73,4944
Polymers73,0062
Non-polymers4892
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-12 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.000, 84.437, 58.020
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


Mass: 36502.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: birA / Plasmid: Klpnc.17896.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W7ZMT5
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus H2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM ...Details: Morpheus H2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine 20mg/ml protein and 4 mM Biotin, KlpnC.17896.a.B1.PW39036 at 30 mg/mL. Tray: Liu-S-043 drop C5, Puck: PSL0113, Cryo: 150% Morpheus G3.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→47.82 Å / Num. obs: 17266 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Χ2: 1 / Net I/σ(I): 9.7 / Num. measured all: 114603
Reflection shellResolution: 2.9→3.08 Å / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.158 / Num. measured all: 17046 / Num. unique obs: 2720 / CC1/2: 0.555 / Rpim(I) all: 0.502 / Rrim(I) all: 1.265 / Χ2: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.82 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3059 838 4.87 %
Rwork0.2422 --
obs0.2451 17200 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 32 7 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034847
X-RAY DIFFRACTIONf_angle_d0.6536577
X-RAY DIFFRACTIONf_dihedral_angle_d18.8041781
X-RAY DIFFRACTIONf_chiral_restr0.048752
X-RAY DIFFRACTIONf_plane_restr0.005846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.080.37591250.3512678X-RAY DIFFRACTION99
3.08-3.320.35961390.30312667X-RAY DIFFRACTION100
3.32-3.650.33491460.28262701X-RAY DIFFRACTION99
3.65-4.180.30191530.23982701X-RAY DIFFRACTION100
4.18-5.270.28511300.21082763X-RAY DIFFRACTION100
5.27-47.820.27851450.21272852X-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)
12.30320.95750.44617.1394-0.66921.3872-0.30170.52840.592-0.00490.3410.3955-0.33330.30170.02830.51480.0458-0.03190.98460.13790.743858.695146.875345.7449
25.8238-0.73470.1151.8524-0.0881.4705-0.2370.00930.1405-0.03570.11620.189-0.0474-0.02480.14470.44380.0139-0.02060.7467-0.02890.453246.02612.50324.4776
30.963-0.9560.4663.25860.57831.3836-0.0969-0.3494-0.71520.0926-0.13890.27750.364-0.2366-0.01980.4368-0.01840.05330.7866-0.02970.558245.27891.664923.6046
43.2188-1.4449-1.63523.5972.00063.9308-0.18970.0514-0.3214-0.1621-0.00390.0814-0.0424-0.08660.21860.4287-0.03480.03280.5720.05570.536755.9037-1.989718.7806
56.6494-1.0906-1.01313.05640.17010.96730.0092-0.0750.20320.25540.04760.66060.1238-0.27750.04040.57740.02390.14020.8586-0.05730.693623.31613.508836.4248
63.97791.4451-0.76146.3453-1.09043.52820.0672-0.00190.51890.1259-0.02490.2895-0.2336-0.2774-0.05810.32770.01680.00110.68750.02760.387758.215123.531756.5585
75.80321.0109-2.06364.484-1.03253.60.02940.1342-0.1323-0.0176-0.125-0.68090.04810.24570.12240.35790.0081-0.0780.5302-0.01190.353469.220523.037757.2235
81.9284-0.60730.30622.4477-0.67221.3943-0.00890.0125-0.1823-0.17790.0112-0.23720.24110.13880.14030.3596-0.0030.06710.6644-0.00450.498771.455112.49361.9453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 234 )
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 317 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 164 )
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 234 )
8X-RAY DIFFRACTION8chain 'B' and (resid 235 through 317 )

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