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- PDB-4ofs: Crystal structure of a truncated catalytic core of the 2-oxoacid ... -

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Basic information

Entry
Database: PDB / ID: 4ofs
TitleCrystal structure of a truncated catalytic core of the 2-oxoacid dehydrogenase multienzyme complex from Thermoplasma acidophilum
ComponentsProbable lipoamide acyltransferase
KeywordsOXIDOREDUCTASE / ALPHA BETA FOLD/ACYL-TRANSFERASE/TRANSFERASE / 2-Oxoacid dehydrogenase
Function / homology
Function and homology information


acyltransferase activity / identical protein binding / cytoplasm
Similarity search - Function
Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. ...Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Probable lipoamide acyltransferase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsMarrot, N.L. / Marshall, J.J.T. / Svergun, D.I. / Crennell, S.J. / Hough, D.W. / van den Elsen, J.M.H. / Danson, M.J.
Citation
Journal: Biochem.J. / Year: 2014
Title: Why are the 2-oxoacid dehydrogenase complexes so large? Generation of an active trimeric complex.
Authors: Marrott, N.L. / Marshall, J.J. / Svergun, D.I. / Crennell, S.J. / Hough, D.W. / van den Elsen, J.M. / Danson, M.J.
#1: Journal: Febs J. / Year: 2012
Title: The catalytic core of an archaeal 2-oxoacid dehydrogenase multienzyme complex is a 42-mer protein assembly.
Authors: Marrott, N.L. / Marshall, J.J. / Svergun, D.I. / Crennell, S.J. / Hough, D.W. / Danson, M.J. / van den Elsen, J.M.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable lipoamide acyltransferase
B: Probable lipoamide acyltransferase
C: Probable lipoamide acyltransferase
D: Probable lipoamide acyltransferase
E: Probable lipoamide acyltransferase
F: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)149,1486
Polymers149,1486
Non-polymers00
Water0
1
A: Probable lipoamide acyltransferase
B: Probable lipoamide acyltransferase
C: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,5743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-45 kcal/mol
Surface area26120 Å2
MethodPISA
2
D: Probable lipoamide acyltransferase
E: Probable lipoamide acyltransferase
F: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)74,5743
Polymers74,5743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-47 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.151, 107.151, 238.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.012275, -0.2428, 0.969999), (0.96839, -0.238816, -0.072033), (0.249141, 0.940221, 0.232194)39.54844, -73.48106, 10.78356
3given(0.013688, 0.967542, 0.252341), (-0.252056, -0.240876, 0.937255), (0.967616, -0.076433, 0.240578)67.85544, -17.49582, -46.03392
4given(0.48565, -0.874153, -5.5E-5), (-0.764747, -0.424897, 0.484381), (-0.423447, -0.235198, -0.874857)51.26679, 19.12368, 5.05689
5given(-0.838959, -0.484594, 0.247622), (-0.335687, 0.102694, -0.936359), (0.428324, -0.86869, -0.248827)88.34026, -30.16727, 3.14593
6given(-0.223733, -0.120047, -0.967229), (0.689495, -0.720899, -0.070015), (-0.688869, -0.682564, 0.244061)40.46842, -29.46097, 42.29595
DetailsThis is the truncated version of the enzyme that naturally forms a 42-mer multienzyme complex. In this structure a crystallographic dimer of trimer is observed which only assembles into an active trimer in solution

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Components

#1: Protein
Probable lipoamide acyltransferase


Mass: 24857.930 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: Ta1436 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3
References: UniProt: Q9HIA5, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% (w/v) PEG4K; 3% (w/v) PGA; 0.1M Na Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. all: 12902 / Num. obs: 12274 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.06
Reflection shellResolution: 4.1→4.17 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.48 / % possible all: 97.4

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Processing

Software
NameVersionClassification
GDAdata collection
BALBESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RQC

3rqc


Resolution: 4.1→48.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 164.294 / SU ML: 0.894 / Cross valid method: THROUGHOUT / ESU R Free: 1.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 628 4.9 %RANDOM
Rwork0.21222 ---
obs0.21566 12274 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 4.1→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10241 0 0 0 10241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910391
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.97714024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72651279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36223.437451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.471151995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2171591
X-RAY DIFFRACTIONr_chiral_restr0.1190.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217551
LS refinement shellResolution: 4.104→4.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 46 -
Rwork0.365 759 -
obs--95.04 %
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)
14.6885-0.5698-0.85294.59720.15293.46330.007-0.21050.0483-0.0011-0.04550.84070.3202-0.25360.03860.3937-0.1015-0.19490.1541-0.11230.439745.7695-14.768826.4812
22.7577-0.4496-1.26894.5626-0.35184.024-0.14390.0806-0.4231-0.4687-0.0653-0.34030.7610.68390.20920.53190.0063-0.03930.3137-0.11820.303869.3892-27.605714.4263
33.6055-0.27950.09481.5228-0.6014.6338-0.13350.42540.489-0.61670.09970.0618-0.12790.1570.03370.4973-0.1405-0.18710.2617-0.15390.517561.0684-0.76925.5467
44.8517-0.4294-0.06283.45860.66944.8-0.21040.25330.6644-0.21110.1128-0.3831-0.64090.48280.09760.4119-0.1556-0.23540.1548-0.04970.533940.47411.7652-30.8403
53.8033-0.882-0.57862.03610.07944.0397-0.153-0.64540.24550.88350.02110.3943-0.4415-0.380.13190.71140.0251-0.04150.2346-0.24620.694219.8366-0.3791-9.9142
63.95350.4476-0.77952.8255-0.92142.22670.14650.33240.9469-0.0793-0.08270.5503-0.5205-0.4141-0.06380.70580.0978-0.19860.3407-0.15370.995513.97313.9719-34.6826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 219
2X-RAY DIFFRACTION2B6 - 219
3X-RAY DIFFRACTION3C6 - 219
4X-RAY DIFFRACTION4D6 - 219
5X-RAY DIFFRACTION5E6 - 219
6X-RAY DIFFRACTION6F5 - 219

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