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- PDB-5t8u: Crystal structure of P. falciparum LipL1 in complex lipoate -

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Basic information

Entry
Database: PDB / ID: 5t8u
TitleCrystal structure of P. falciparum LipL1 in complex lipoate
ComponentsLipoate-protein ligase 1Lipoate–protein ligase
KeywordsLIGASE / Lipoylation
Function / homology
Function and homology information


Glyoxylate metabolism and glycine degradation / lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / lipid metabolic process / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein 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 / 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
LIPOIC ACID / Lipoate--protein ligase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsGuerra, A.J. / Afanador, G.A. / Prigge, S.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI065853 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI110028 United States
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum.
Authors: Guerra, A.J. / Afanador, G.A. / Prigge, S.T.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoate-protein ligase 1
B: Lipoate-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8224
Polymers84,4102
Non-polymers4132
Water1,51384
1
A: Lipoate-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4112
Polymers42,2051
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoate-protein ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4112
Polymers42,2051
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.240, 120.240, 134.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lipoate-protein ligase 1 / Lipoate–protein ligase


Mass: 42204.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF3D7_1314600 / Plasmid: pMALcHT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q8IEG9, EC: 2.7.7.63
#2: Chemical ChemComp-LPA / LIPOIC ACID / 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid / Lipoic acid


Mass: 206.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5M Ammonium Sulfate, 20% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127085 Å / Relative weight: 1
ReflectionResolution: 2.324→48.574 Å / Num. obs: 48667 / % possible obs: 96 % / Redundancy: 5.9 % / Biso Wilson estimate: 53.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1391 / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
PHENIX(1.11_2558: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7A

3a7a


Resolution: 2.324→48.574 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3017 2309 4.88 %
Rwork0.2727 --
obs0.2742 47306 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.324→48.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 24 84 5594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025628
X-RAY DIFFRACTIONf_angle_d0.4697628
X-RAY DIFFRACTIONf_dihedral_angle_d13.0673303
X-RAY DIFFRACTIONf_chiral_restr0.041850
X-RAY DIFFRACTIONf_plane_restr0.002984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3239-2.37450.45481070.52362451X-RAY DIFFRACTION85
2.3745-2.42970.44091520.42822848X-RAY DIFFRACTION100
2.4297-2.49050.43951160.42072876X-RAY DIFFRACTION99
2.4905-2.55780.42631330.42172931X-RAY DIFFRACTION100
2.5578-2.63310.46171590.42322830X-RAY DIFFRACTION100
2.6331-2.7180.6439960.56671982X-RAY DIFFRACTION69
2.718-2.81520.38261600.35752918X-RAY DIFFRACTION100
2.8152-2.92790.38051450.33572869X-RAY DIFFRACTION100
2.9279-3.06110.34451800.31772864X-RAY DIFFRACTION99
3.0611-3.22250.34511510.31532881X-RAY DIFFRACTION100
3.2225-3.42430.31831580.30672890X-RAY DIFFRACTION100
3.4243-3.68860.36111200.29572832X-RAY DIFFRACTION97
3.6886-4.05970.29771420.25762864X-RAY DIFFRACTION97
4.0597-4.64670.23481400.18512951X-RAY DIFFRACTION100
4.6467-5.85280.21911620.19432955X-RAY DIFFRACTION100
5.8528-48.58470.23051880.20383055X-RAY DIFFRACTION100
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)
12.43490.1074-0.48922.64570.79452.5506-0.07090.0068-0.22740.05570.04650.01170.03090.23590.02590.4797-0.05270.02220.7208-0.00110.368583.0744683.7757297.2713
21.1360.0148-1.04581.5637-0.41235.5795-0.10610.7139-0.0966-0.359-0.02980.290.1091-0.61680.14680.4677-0.0351-0.06440.9642-0.03910.49876.5886685.2889279.3867
33.2411.0914-0.16823.8162-0.66160.86030.13240.03880.04450.0766-0.0817-0.1044-0.11030.1226-0.04480.4677-0.04020.01280.7049-0.07350.3401108.8746688.1774270.422
40.8297-0.1469-0.25562.53811.34831.46080.0350.0610.05960.0016-0.0553-0.0041-0.35390.07990.01110.6457-0.009-0.03250.7066-0.0090.3767103.1307698.5947276.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 370 )
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 191 )
4X-RAY DIFFRACTION4chain 'B' and (resid 192 through 370 )

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