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- PDB-3r07: Structural analysis of an archaeal lipoylation system. A bi-parti... -

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Basic information

Entry
Database: PDB / ID: 3r07
TitleStructural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum
Components
  • Lipoate-protein ligase A subunit 1Lipoate–protein ligase
  • Putative lipoate-protein ligase A subunit 2Lipoate–protein ligase
KeywordsTRANSFERASE / Adenylate-forming enzyme / Ligase / bi-partite / ATP-binding
Function / homology
Function and homology information


lipoate-protein ligase / lipoate-protein ligase activity / lipoic acid binding / protein lipoylation / ligase activity / protein-containing complex / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / 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 ...Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / 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
ACETATE ION / Lipoate-protein ligase A subunit 1 / Lipoate-protein ligase A subunit 2
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPosner, M.G. / Upadhyay, U. / Crennell, S.
CitationJournal: To be Published
Title: Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum
Authors: Posner, M.G. / Upadhyay, A. / Crennell, S. / Danson, M.J. / Bagby, S.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Structure summary
Revision 1.2Nov 6, 2019Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _pdbx_database_related.db_name / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Lipoate-protein ligase A subunit 1
C: Putative lipoate-protein ligase A subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6116
Polymers43,2562
Non-polymers3544
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.570, 118.570, 72.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 32695.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Co-expression
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: lplA, Ta0514 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKT1, EC: 2.7.7.63
#2: Protein Putative lipoate-protein ligase A subunit 2 / Lipoate–protein ligase / Lipoate--protein ligase subunit 2


Mass: 10561.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Co-expression
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta0513, Ta0513m / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKT2, EC: 2.7.7.63
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 291 K / pH: 4.6
Details: 40% v/v MPD, 0.1M sodium acetate, 0.02M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2009 / Details: VORTEX FLUORESCENCE DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→38.81 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ARS

2ars


Resolution: 2.7→38.81 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.005 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 789 5 %RANDOM
Rwork0.198 ---
obs0.2 15063 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 24 47 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9713853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47823.611144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13915538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5921527
X-RAY DIFFRACTIONr_chiral_restr0.0980.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21193
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21910
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0121.51765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74222768
X-RAY DIFFRACTIONr_scbond_it2.42731224
X-RAY DIFFRACTIONr_scangle_it3.8724.51080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 69 -
Rwork0.251 1093 -
obs--100 %

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