2WU5

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant

• PDB DOI: https://doi.org/10.2210/pdb2WU5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2009-09-29 Released: 2010-08-25 
• Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd His71met Mutant

Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 363.3 kDa 
• Atom Count: 25,164 
• Modelled Residue Count: 3,159 
• Deposited Residue Count: 3,210 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A, E, I	588	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12)) Explore P0AC41  Go to UniProtKB:  P0AC41

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT	B, F, J	238	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data) Membrane Entity: Yes
UniProt
Find proteins for P07014 (Escherichia coli (strain K12)) Explore P07014  Go to UniProtKB:  P07014

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT	C, G, K	129	Escherichia coli	Mutation(s): 0  EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P69054 (Escherichia coli (strain K12)) Explore P69054  Go to UniProtKB:  P69054

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT	D, H, L	115	Escherichia coli	Mutation(s): 1  EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12)) Explore P0AC44  Go to UniProtKB:  P0AC44

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	CA [auth I], M [auth A], U [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	AA [auth G], IA [auth K], S [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SF4	GA [auth J], Q [auth B], Y [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	HA [auth J], R [auth B], Z [auth F]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
CBE	BA [auth G], JA [auth K], T [auth C]	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE C12 H13 N O2 S GYSSRZJIHXQEHQ-UHFFFAOYSA-N
FES	FA [auth J], P [auth B], X [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
TEO	DA [auth I], N [auth A], V [auth E]	MALATE LIKE INTERMEDIATE C4 H4 O5 QFBHYOKSQPPXHZ-UWTATZPHSA-L
NA	EA [auth I], O [auth A], W [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.06	α = 90
b = 183.82	β = 90
c = 203.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-25 
Deposition Author(s): Ruprecht, J., Yankovskaya, V., Maklashina, E., Iwata, S., Cecchini, G.

Revision History  

• Version 1.0: 2010-08-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Advisory, Derived calculations, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description