2WS3

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD Tyr83Phe mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Succinate Dehydrogenase Activity

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 B-556 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 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

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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: 3.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.850α = 90.00
b = 184.710β = 90.00
c = 203.310γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

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