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- PDB-6aon: 1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehy... -

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Basic information

Entry
Database: PDB / ID: 6aon
Title1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehydrogenase Complex Subunit Dihydrolipoamide Dehydrogenase from Bordetella pertussis in Complex with FAD
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase / FAD
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / flavin adenine dinucleotide binding / metal ion binding
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 ...Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / McChesney, C. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.4Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4845
Polymers100,8732
Non-polymers1,6113
Water19,5281084
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 5U8U
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-61 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.801, 68.801, 199.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Dihydrolipoyl dehydrogenase / 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase


Mass: 50436.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: odhL, BP1126 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7VZ16, dihydrolipoyl dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5 against screen (0.2 M calcium acetate, 20% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2017 / Details: C(111)
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 96213 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.041 / Rsym value: 0.086 / Χ2: 1.023 / Net I/σ(I): 14.7
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2 / Num. unique obs: 4725 / CC1/2: 0.648 / Rpim(I) all: 0.378 / Rsym value: 0.781 / Χ2: 1.009 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5U8U

5u8u


Resolution: 1.72→29.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.899 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20529 4844 5.1 %RANDOM
Rwork0.1695 ---
obs0.17133 90615 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.72→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7026 0 107 1084 8217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197538
X-RAY DIFFRACTIONr_bond_other_d0.0010.027106
X-RAY DIFFRACTIONr_angle_refined_deg1.421.96910268
X-RAY DIFFRACTIONr_angle_other_deg0.848316503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.80351001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46124.983297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.828151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.651533
X-RAY DIFFRACTIONr_chiral_restr0.0830.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.028596
X-RAY DIFFRACTIONr_gen_planes_other0.020.021455
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.741.5143926
X-RAY DIFFRACTIONr_mcbond_other0.7391.5143925
X-RAY DIFFRACTIONr_mcangle_it1.2072.274953
X-RAY DIFFRACTIONr_mcangle_other1.2072.274954
X-RAY DIFFRACTIONr_scbond_it1.1661.683612
X-RAY DIFFRACTIONr_scbond_other1.1661.683613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8542.4495316
X-RAY DIFFRACTIONr_long_range_B_refined5.2720.0779014
X-RAY DIFFRACTIONr_long_range_B_other4.86118.7768660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 356 -
Rwork0.261 6624 -
obs--97.03 %
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)
10.5812-0.7320.02141.0228-0.21140.56810.04290.0625-0.0108-0.0782-0.0221-0.0085-0.0261-0.0791-0.02080.055-0.0021-0.00040.0742-0.00110.081119.937848.3443105.778
20.3176-0.2142-0.18630.8534-0.2950.58560.01240.0361-0.0527-0.02540.02760.0882-0.0135-0.1148-0.03990.00590.0038-0.01080.04640.00470.049313.359451.796109.6385
34.1895-0.4195-2.16040.9316-0.61492.09460.074-0.26380.20630.02010.0634-0.0156-0.23670.0729-0.13740.14690.01830.02570.0337-0.03010.048612.888771.7033123.0101
40.5694-0.2522-0.10980.54250.03940.71080.0245-0.0648-0.00230.01530.008-0.0272-0.05310.0632-0.03250.0104-0.01540.00040.03040.00730.041825.114150.6773119.53
51.04130.34850.01822.1581-0.23420.9860.1673-0.08740.07470.3412-0.18420.0705-0.04810.04210.0170.0935-0.05540.01330.0349-0.010.023438.520873.3396109.1074
60.97330.64640.280.46940.06520.49070.0467-0.09690.11760.0547-0.04880.0774-0.0319-0.06990.00210.04170.01040.00650.0558-0.00890.063830.349985.691390.7862
71.24760.76470.76430.92070.30481.6105-0.05330.05390.0562-0.0544-0.0021-0.0241-0.21330.14360.05540.0478-0.01220.00720.01750.01590.044544.028794.437785.3057
81.3785-1.27410.49251.8818-1.0871.51920.14270.0599-0.0261-0.2731-0.08970.05670.1678-0.0374-0.05290.07450.005-0.02230.0187-0.00490.048426.299572.666570.5211
91.44980.05850.74071.17290.0571.26630.04050.0957-0.0707-0.0155-0.0302-0.14840.01750.2497-0.01030.00650.00560.00930.06240.00060.055952.791883.633984.6576
100.65120.1292-0.12990.7115-0.06820.5504-0.0350.00020.0053-0.03120.03010.01270.0049-0.01190.00490.0229-0.00850.00840.0142-0.00130.037837.509957.858593.1075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 74
2X-RAY DIFFRACTION2A75 - 209
3X-RAY DIFFRACTION3A210 - 265
4X-RAY DIFFRACTION4A266 - 366
5X-RAY DIFFRACTION5A367 - 475
6X-RAY DIFFRACTION6B3 - 102
7X-RAY DIFFRACTION7B103 - 178
8X-RAY DIFFRACTION8B179 - 277
9X-RAY DIFFRACTION9B278 - 351
10X-RAY DIFFRACTION10B352 - 475

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