[English] 日本語
Yorodumi
- PDB-6aon: 1.72 Angstrom Resolution Crystal Structure of 2-Oxoglutarate Dehy... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more