2WU5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
A, E, I
588Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhA
EC: 1.3.5.1
Find proteins for P0AC41 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
B, F, J
238Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhB
EC: 1.3.5.1
Find proteins for P07014 (Escherichia coli (strain K12))
Go to UniProtKB:  P07014
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
C, G, K
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sdhC (cybA)
Find proteins for P69054 (Escherichia coli (strain K12))
Go to UniProtKB:  P69054
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT
D, H, L
115Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: sdhD
Find proteins for P0AC44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC44
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
B, F, J
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
B, F, J
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, E, I
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, E, I
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
B, F, J
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C, G, K
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
TEO
Query on TEO

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Download CCD File 
A, E, I
MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
 Ligand Interaction
CBE
Query on CBE

Download SDF File 
Download CCD File 
C, G, K
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
5,6-DIHYDRO-2-METHYL-1,4-OXATHIIN-3-CARBOXANILID; CARBOXIN; CBX
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.803 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.060α = 90.00
b = 183.820β = 90.00
c = 203.420γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance