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- PDB-1x2g: Crystal Structure of Lipate-Protein Ligase A from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1x2g
TitleCrystal Structure of Lipate-Protein Ligase A from Escherichia coli
ComponentsLipoate-protein ligase A
KeywordsLIGASE / lipoate-protein ligase / lipoic acid / protein acylation / post-translational modification
Function / homology
Function and homology information


lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / ATP binding / cytoplasm / cytosol
Similarity search - Function
Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / CO dehydrogenase flavoprotein, C-terminal 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 ...Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / CO dehydrogenase flavoprotein, C-terminal 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) / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoate-protein ligase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsFujiwara, K. / Toma, S. / Okamura-Ikeda, K. / Motokawa, Y. / Nakagawa, A. / Taniguchi, H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of lipoate-protein ligase A from Escherichia coli: Determination of the lipoic acid-binding site
Authors: Fujiwara, K. / Toma, S. / Okamura-Ikeda, K. / Motokawa, Y. / Nakagawa, A. / Taniguchi, H.
History
DepositionApr 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoate-protein ligase A
B: Lipoate-protein ligase A
C: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)114,2253
Polymers114,2253
Non-polymers00
Water9,548530
1
A: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)38,0751
Polymers38,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)38,0751
Polymers38,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)38,0751
Polymers38,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Lipoate-protein ligase A
B: Lipoate-protein ligase A
C: Lipoate-protein ligase A

A: Lipoate-protein ligase A
B: Lipoate-protein ligase A
C: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)228,4516
Polymers228,4516
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area18790 Å2
ΔGint-24 kcal/mol
Surface area80420 Å2
MethodPISA
5
A: Lipoate-protein ligase A
C: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)76,1502
Polymers76,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-5 kcal/mol
Surface area29030 Å2
MethodPISA
6
B: Lipoate-protein ligase A

B: Lipoate-protein ligase A


Theoretical massNumber of molelcules
Total (without water)76,1502
Polymers76,1502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4000 Å2
ΔGint-2 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.000, 112.800, 289.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lipoate-protein ligase A


Mass: 38075.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: P32099, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ethylene glycol, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 / Date: May 31, 2003 / Details: mirror
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 52725 / Num. obs: 52725 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.92 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.858 / SU ML: 0.161 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.235 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23337 2686 5.1 %RANDOM
Rwork0.17099 ---
all0.1742 49805 --
obs0.1742 49805 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.235 Å0.303 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 0 530 8425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0228064
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.831.94510928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27823.596406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.085151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5141573
X-RAY DIFFRACTIONr_chiral_restr0.1250.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026236
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.23651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25457
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1321.55085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90327951
X-RAY DIFFRACTIONr_scbond_it2.97133376
X-RAY DIFFRACTIONr_scangle_it4.6224.52977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.4 Å / Num. reflection Rwork: 3551 / Total num. of bins used: 20

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