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- PDB-3a7u: Crystal structure of the bovine lipoyltransferase in its unligand... -

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Basic information

Entry
Database: PDB / ID: 3a7u
TitleCrystal structure of the bovine lipoyltransferase in its unliganded form
ComponentsLipoyltransferase 1, mitochondrial
KeywordsTRANSFERASE / lipoic acid / Acyltransferase / Mitochondrion / Transit peptide
Function / homology
Function and homology information


lipoyl amidotransferase / lipoyltransferase activity / Glyoxylate metabolism and glycine degradation / lipoate-protein ligase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / protein modification process / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Lipoyltransferase/lipoate-protein ligase / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / 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) / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoyl amidotransferase LIPT1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsFujiwara, K. / Hosaka, H. / Nakagawa, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A.
Authors: Fujiwara, K. / Maita, N. / Hosaka, H. / Okamura-Ikeda, K. / Nakagawa, A. / Taniguchi, H.
History
DepositionOct 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoyltransferase 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)39,2151
Polymers39,2151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.175, 91.175, 232.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Lipoyltransferase 1, mitochondrial / Lipoate-protein ligase / Lipoate biosynthesis protein / Lipoyl ligase


Mass: 39214.797 Da / Num. of mol.: 1 / Fragment: UNP residues 27-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LIPT1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O46419, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.44→50 Å / Num. all: 8169 / Num. obs: 8169 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 44
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 14 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E5A

2e5a


Resolution: 3.44→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / SU B: 75.132 / SU ML: 0.544 / SU Rfree: 0.666 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.666 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31839 605 7.5 %RANDOM
Rwork0.24224 ---
obs0.24779 7452 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 3.44→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 0 0 2600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8631.9423608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0395323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84324.545121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64315472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7991512
X-RAY DIFFRACTIONr_chiral_restr0.0620.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.51617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70422633
X-RAY DIFFRACTIONr_scbond_it0.48931042
X-RAY DIFFRACTIONr_scangle_it0.8914.5975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.444→3.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 44 -
Rwork0.303 480 -
obs--91.13 %
Refinement TLS params.Method: refined / Origin x: -12.8283 Å / Origin y: 34.1965 Å / Origin z: -16.3986 Å
111213212223313233
T0.155 Å2-0.0565 Å20.0934 Å2-0.0725 Å2-0.0578 Å2--0.1082 Å2
L2.745 °2-0.8017 °2-2.2025 °2-0.2587 °20.7587 °2--2.8956 °2
S0.158 Å °0.2146 Å °0.0813 Å °-0.0032 Å °-0.052 Å °-0.0243 Å °-0.0363 Å °-0.2421 Å °-0.1059 Å °

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