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- PDB-3rqc: Crystal structure of the catalytic core of the 2-oxoacid dehydrog... -

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Basic information

Entry
Database: PDB / ID: 3rqc
TitleCrystal structure of the catalytic core of the 2-oxoacid dehydrogenase multienzyme complex from Thermoplasma acidophilum
ComponentsProbable lipoamide acyltransferase
KeywordsTRANSFERASE / Alpha Beta fold / acyl-transferase
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 DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å
AuthorsMarrott, N.L. / Crennell, S.J. / Hough, D.W. / Danson, M.J. / van den Elsen, J.M.H.
CitationJournal: 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
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
G: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)178,4287
Polymers178,4287
Non-polymers00
Water0
1
A: Probable lipoamide acyltransferase
B: Probable lipoamide acyltransferase
C: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)76,4693
Polymers76,4693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-50 kcal/mol
Surface area28090 Å2
MethodPISA
2
D: Probable lipoamide acyltransferase
E: Probable lipoamide acyltransferase
F: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)76,4693
Polymers76,4693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-38 kcal/mol
Surface area28840 Å2
MethodPISA
3
G: Probable lipoamide acyltransferase

G: Probable lipoamide acyltransferase

G: Probable lipoamide acyltransferase


Theoretical massNumber of molelcules
Total (without water)76,4693
Polymers76,4693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area8340 Å2
ΔGint-39 kcal/mol
Surface area28000 Å2
MethodPISA
4
A: Probable lipoamide acyltransferase
B: Probable lipoamide acyltransferase
C: Probable lipoamide acyltransferase
D: Probable lipoamide acyltransferase
E: Probable lipoamide acyltransferase
F: Probable lipoamide acyltransferase
G: Probable lipoamide acyltransferase
x 6


Theoretical massNumber of molelcules
Total (without water)1,070,56742
Polymers1,070,56742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area157010 Å2
ΔGint-781 kcal/mol
Surface area365880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.840, 204.840, 441.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41E
12B
22C
32F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 10 - 210 / Label seq-ID: 10 - 210

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
115AA
215DD
315GG
415EE
124BB
224CC
324FF

NCS ensembles :
ID
1
2
DetailsBasic biological unit is a trimer. In some bacterial and eukaryotic complexes multiple E2 polypeptide chains associate into octahedral (24-meric) or icosahedral (60-meric) configurations. The T. acidophilum E2 core structure deposited here has an exceptional configuration of 42 chains.

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Components

#1: Protein
Probable lipoamide acyltransferase


Mass: 25489.695 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
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: 5 Å3/Da / Density % sol: 75.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% MPD, 0.2M NaCl, 0.1M Na Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010
RadiationMonochromator: Double crystal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 4.01→44.95 Å / Num. all: 29696 / Num. obs: 28168 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 4→4.14 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAF

1eaf


Resolution: 4.01→44.95 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.834 / SU B: 126.525 / SU ML: 0.763 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.878 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32773 1504 5.1 %RANDOM
Rwork0.25291 ---
all0.25672 ---
obs0.25672 28168 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 4.01→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12157 0 0 0 12157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212340
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.97616659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.25651515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13723.321533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.989152364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.10615108
X-RAY DIFFRACTIONr_chiral_restr0.1310.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218958
X-RAY DIFFRACTIONr_mcbond_it0.2631.57582
X-RAY DIFFRACTIONr_mcangle_it0.514212399
X-RAY DIFFRACTIONr_scbond_it0.7334758
X-RAY DIFFRACTIONr_scangle_it1.3034.54260
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A804medium positional0.450.5
11D804medium positional0.460.5
11G804medium positional0.440.5
11E804medium positional0.410.5
22B1601medium positional0.760.5
22C1601medium positional0.740.5
22F1601medium positional0.680.5
11A797loose positional15
11D797loose positional0.965
11G797loose positional0.985
11E797loose positional1.025
11A804medium thermal0.342
11D804medium thermal0.272
11G804medium thermal0.282
11E804medium thermal0.272
22B1601medium thermal0.412
22C1601medium thermal0.412
22F1601medium thermal0.352
11A797loose thermal0.5410
11D797loose thermal0.3910
11G797loose thermal0.4410
11E797loose thermal0.4310
LS refinement shellResolution: 4.007→4.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 114 -
Rwork0.316 2038 -
obs--100 %
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)
16.0209-1.997-2.85446.0080.7215.97060.0777-0.1087-0.46570.0034-0.1460.15570.07090.06420.06840.02940.01280.00480.0623-0.03810.1153-29.078-76.6841-15.3106
25.59360.2609-0.38564.8469-2.03596.16920.094-0.1770.25750.0958-0.0739-0.3718-1.14020.8455-0.02010.4621-0.13570.10760.159-0.05850.2376-18.1664-52.8377-29.1219
34.75360.41761.20935.06881.49377.2925-0.13790.310.5486-0.35820.10320.493-0.6411-0.51270.03470.20910.14620.06590.20460.09850.2193-45.9671-60.5943-33.6904
45.5333-0.01930.68396.38420.3358.6440.08340.2191-0.5023-0.6643-0.00780.56640.9143-1.3526-0.07570.4169-0.1151-0.12140.59950.14290.4982-78.7386-100.6132-78.4905
56.26391.11871.51475.72170.14927.40550.2375-0.88640.180.4913-0.02660.7429-0.0282-0.9579-0.21090.12280.13980.140.7320.08590.3141-72.8745-81.1525-56.6742
66.20390.8339-0.13866.0623-0.53736.8789-0.0482-0.04720.5598-0.5550.22960.5013-1.0416-0.5292-0.18150.35060.2528-0.01280.49580.1140.3679-70.5235-73.2284-85.5722
79.0511-1.06532.11446.4606-0.10597.0097-0.2466-0.43810.7990.71380.1-0.0803-0.5544-0.02980.14670.16690.03710.00930.1096-0.12590.2272-4.3275-101.6379-2.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 222
2X-RAY DIFFRACTION2B5 - 222
3X-RAY DIFFRACTION3C3 - 222
4X-RAY DIFFRACTION4D5 - 222
5X-RAY DIFFRACTION5E6 - 222
6X-RAY DIFFRACTION6F8 - 222
7X-RAY DIFFRACTION7G6 - 222

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