[English] 日本語
Yorodumi
- PDB-6b58: FrdA-SdhE assembly intermediate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b58
TitleFrdA-SdhE assembly intermediate
Components
  • FAD assembly factor SdhE
  • Fumarate reductase flavoprotein subunit
KeywordsFLAVOPROTEIN / FrdA / assembly intermediate / complex / respiration
Function / homology
Function and homology information


respiratory chain complex II assembly / plasma membrane fumarate reductase complex / succinate dehydrogenase activity / succinate metabolic process / fermentation / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / bacterial-type flagellum assembly ...respiratory chain complex II assembly / plasma membrane fumarate reductase complex / succinate dehydrogenase activity / succinate metabolic process / fermentation / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / bacterial-type flagellum assembly / FAD binding / flavin adenine dinucleotide binding / electron transfer activity / DNA damage response / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Fumarate reductase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal ...Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Fumarate reductase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / : / MALONATE ION / DI(HYDROXYETHYL)ETHER / Fumarate reductase flavoprotein subunit / FAD assembly factor SdhE / FAD assembly factor SdhE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å
AuthorsSharma, P. / Iverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061606 United States
Department of Veterans AffairsBX001077 United States
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of an assembly intermediate of respiratory Complex II.
Authors: Sharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionSep 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
B: FAD assembly factor SdhE
C: Fumarate reductase flavoprotein subunit
D: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,18126
Polymers146,3344
Non-polymers2,84722
Water1,13563
1
A: Fumarate reductase flavoprotein subunit
B: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65315
Polymers73,1672
Non-polymers1,48613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-11 kcal/mol
Surface area23760 Å2
MethodPISA
2
C: Fumarate reductase flavoprotein subunit
D: FAD assembly factor SdhE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,52811
Polymers73,1672
Non-polymers1,3619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-17 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.640, 63.330, 175.580
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Fumarate reductase flavoprotein subunit


Mass: 63477.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00363, fumarate reductase (quinol)
#2: Protein FAD assembly factor SdhE


Mass: 9689.108 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P64561, UniProt: P64559*PLUS

-
Non-polymers , 8 types, 85 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 90 mM Bis-Tris pH 5.5, 100 mM NH4CH3COO, 20% PEG 10,000 and 50mM NaMalonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 41620 / % possible obs: 96.8 % / Redundancy: 5 % / Net I/σ(I): 11.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF6

1kf6


Resolution: 2.611→37.153 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2025 4.87 %
Rwork0.1914 --
obs0.1946 41598 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.611→37.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9308 0 188 63 9559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019677
X-RAY DIFFRACTIONf_angle_d1.06813105
X-RAY DIFFRACTIONf_dihedral_angle_d6.1336594
X-RAY DIFFRACTIONf_chiral_restr0.0571430
X-RAY DIFFRACTIONf_plane_restr0.0071730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6113-2.67660.29841230.25492561X-RAY DIFFRACTION88
2.6766-2.74890.34851490.27262825X-RAY DIFFRACTION97
2.7489-2.82980.41661500.27422823X-RAY DIFFRACTION97
2.8298-2.92110.35271130.26232875X-RAY DIFFRACTION97
2.9211-3.02550.34141410.23262872X-RAY DIFFRACTION98
3.0255-3.14650.29871360.2222857X-RAY DIFFRACTION98
3.1465-3.28970.31581510.22152845X-RAY DIFFRACTION97
3.2897-3.4630.26081630.20512588X-RAY DIFFRACTION89
3.463-3.67980.27071370.17572845X-RAY DIFFRACTION97
3.6798-3.96360.20411440.16792927X-RAY DIFFRACTION99
3.9636-4.36190.23211600.162893X-RAY DIFFRACTION99
4.3619-4.99180.2181750.15732892X-RAY DIFFRACTION98
4.9918-6.28420.23531500.19052880X-RAY DIFFRACTION97
6.2842-37.15680.21211330.17512890X-RAY DIFFRACTION94

+
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