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- PDB-2c8m: Structure of protein Ta0514, putative lipoate protein ligase from... -

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Basic information

Entry
Database: PDB / ID: 2c8m
TitleStructure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid
ComponentsLIPOATE-PROTEIN LIGASE A
KeywordsLIGASE / LIPOYLATION
Function / homology
Function and homology information


lipoate-protein ligase / lipoate-protein ligase activity / lipoic acid binding / protein lipoylation / protein-containing complex / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / 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
LIPOIC ACID / Lipoate-protein ligase A subunit 1
Similarity search - Component
Biological speciesTHERMOPLASMA ACIDOPHILUM (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMcManus, E. / Perham, R.N. / Luisi, B.F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of a Putative Lipoate Protein Ligase from Thermoplasma Acidophilum and the Mechanism of Target Selection for Post-Translational Modification.
Authors: Mcmanus, E. / Luisi, B.F. / Perham, R.N.
History
DepositionDec 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Dec 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
B: LIPOATE-PROTEIN LIGASE A
C: LIPOATE-PROTEIN LIGASE A
D: LIPOATE-PROTEIN LIGASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4868
Polymers119,6614
Non-polymers8254
Water8,719484
1
A: LIPOATE-PROTEIN LIGASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers29,9151
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LIPOATE-PROTEIN LIGASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers29,9151
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: LIPOATE-PROTEIN LIGASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers29,9151
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: LIPOATE-PROTEIN LIGASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers29,9151
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.377, 117.882, 105.663
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113B1 - 256
2113A1 - 256
1124C1 - 256
2124A1 - 256
1134D1 - 256
2134A1 - 256

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
LIPOATE-PROTEIN LIGASE A


Mass: 29915.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Strain: DSM 1728 / Plasmid: PET 3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HKT1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-LPA / LIPOIC ACID / 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid


Mass: 206.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.95 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: pH 6.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.54
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→53.3 Å / Num. obs: 97539 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 20
Reflection shellResolution: 2→2.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7I

2c7i


Resolution: 1.89→53.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.152 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5132 5 %RANDOM
Rwork0.207 ---
obs0.208 97539 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.02 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.89→53.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7510 0 48 484 8042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.959874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3165965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9523.946294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.716151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5941547
X-RAY DIFFRACTIONr_chiral_restr0.0740.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.23369
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25119
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4750.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5350.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9931.54909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.61927551
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.46432792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9424.52323
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B944tight positional0.120.05
2C1719medium positional0.310.5
3D1631medium positional0.30.5
1B844loose positional0.395
1B944tight thermal0.970.5
2C1719medium thermal5.162
3D1631medium thermal6.172
1B844loose thermal2.8810
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 340
Rwork0.307 6738
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)
10.4227-0.16920.04530.68670.0580.4059-0.0286-0.01660.0343-0.0257-0.0158-0.0159-0.0356-0.02130.0444-0.0493-0.0025-0.0082-0.0299-0.0230.0171-10.9839-8.3058-5.5904
20.32420.2368-0.05041.5717-0.02290.2908-0.02210.0160.00080.0509-0.0256-0.0138-0.01970.01440.0477-0.06610.00070.0069-0.0011-0.0085-0.01376.92415.35798.8885
30.4826-0.38020.3771.2682-0.34871.28390.07320.05110.0792-0.12980.00380.08780.077-0.0098-0.0770.02630.02070.00010.00190.0777-0.1159-18.9721-4.4326-41.5365
40.6011-0.11770.16691.5150.46531.4803-0.05080.0356-0.0907-0.0314-0.13360.015-0.0555-0.28370.18440.05250.0450.04160.0418-0.0656-0.1735-16.8954-41.1275-43.6638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 256
2X-RAY DIFFRACTION2B1 - 256
3X-RAY DIFFRACTION3C1 - 256
4X-RAY DIFFRACTION4D1 - 257

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