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- PDB-2qhv: Structural Basis of Octanoic Acid Recognition by Lipoate-Protein ... -

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Basic information

Entry
Database: PDB / ID: 2qhv
TitleStructural Basis of Octanoic Acid Recognition by Lipoate-Protein Ligase B
ComponentsLipoyltransferase
KeywordsTRANSFERASE / globular protein
Function / homology
Function and homology information


lipoyl(octanoyl) transferase / lipoyl(octanoyl) transferase activity / cytoplasm
Similarity search - Function
Octanoyltransferase / Octanoyltransferase, conserved site / Lipoate-protein ligase B signature. / Lipoyl protein ligase A/B catalytic domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) ...Octanoyltransferase / Octanoyltransferase, conserved site / Lipoate-protein ligase B signature. / Lipoyl protein ligase A/B catalytic domain / 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 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTAN-1-OL / Octanoyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKim, D.J. / Lee, S.J. / Kim, H.S. / Kim, K.H. / Lee, H.H. / Yoon, H.J. / Suh, S.W.
CitationJournal: Proteins / Year: 2008
Title: Structural basis of octanoic acid recognition by lipoate-protein ligase B
Authors: Kim, D.J. / Lee, S.J. / Kim, H.S. / Kim, K.H. / Lee, H.H. / Yoon, H.J. / Suh, S.W.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3722
Polymers23,2421
Non-polymers1301
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.670, 63.670, 113.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1012-

HOH

21A-1145-

HOH

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Components

#1: Protein Lipoyltransferase / LipB / Lipoyl-[acyl-carrier-protein]-protein- N-lipoyltransferase / Lipoate-protein ligase B


Mass: 23241.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTC 1746 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS
References: UniProt: Q5SLQ3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM HEPES at pH 7.0, 4.0M lithium chloride, 5%(v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97925, 0.97942, 0.95000
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979421
30.951
ReflectionResolution: 1.6→20 Å / Num. obs: 31493 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.078 / Χ2: 1.527 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.666.70.3630890.484199.9
1.66-1.727.40.28531310.5631100
1.72-1.87.70.21731030.681100
1.8-1.97.60.17331160.841199.9
1.9-2.027.70.13331191.158199.8
2.02-2.177.60.1131541.433199.7
2.17-2.397.60.09631311.807199.4
2.39-2.737.50.08931642.233199.2
2.73-3.447.30.07431832.864198.2
3.44-207.10.05933033.107196.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.499 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3151 10 %RANDOM
Rwork0.207 ---
obs0.21 31469 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 9 206 1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221694
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9682298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37622.475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7215266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9491515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021301
X-RAY DIFFRACTIONr_nbd_refined0.1970.2749
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.211
X-RAY DIFFRACTIONr_mcbond_it0.7681.51065
X-RAY DIFFRACTIONr_mcangle_it1.11921666
X-RAY DIFFRACTIONr_scbond_it1.8783723
X-RAY DIFFRACTIONr_scangle_it2.9834.5632
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 218 -
Rwork0.206 2063 -
obs-2281 99.91 %

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