2IVF | pdb_00002ivf

Ethylbenzene dehydrogenase from Aromatoleum aromaticum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.183 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Ethylbenzene Dehydrogenase from Aromatoleum Aromaticum

Kloer, D.P.Hagel, C.Heider, J.Schulz, G.E.

(2006) Structure 14: 1377

  • DOI: https://doi.org/10.1016/j.str.2006.07.001
  • Primary Citation Related Structures: 
    2IVF

  • PubMed Abstract: 

    Anaerobic degradation of hydrocarbons was discovered a decade ago, and ethylbenzene dehydrogenase was one of the first characterized enzymes involved. The structure of the soluble periplasmic 165 kDa enzyme was established at 1.88 A resolution. It is a heterotrimer. The alpha subunit contains the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, one with an open pyran ring, and an iron-sulfur cluster with a histidine ligand. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. The beta subunit contains four iron-sulfur clusters and is structurally related to ferredoxins. The gamma subunit is the first known protein with a methionine and a lysine as axial heme ligands. The catalytic product was modeled into the active center, showing the reaction geometry. A mechanism consistent with activity and inhibition data of ethylbenzene-related compounds is proposed.


  • Organizational Affiliation
    • Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany.

Macromolecule Content 

  • Total Structure Weight: 178.27 kDa 
  • Atom Count: 12,639 
  • Modeled Residue Count: 1,463 
  • Deposited Residue Count: 1,542 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT976Aromatoleum aromaticum EbN1Mutation(s): 0 
EC: 1.17.99.2
UniProt
Find proteins for Q5P5I0 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1))
Explore Q5P5I0 
Go to UniProtKB:  Q5P5I0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P5I0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT352Aromatoleum aromaticum EbN1Mutation(s): 0 
EC: 1.17.99.2
UniProt
Find proteins for Q5P5I1 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1))
Explore Q5P5I1 
Go to UniProtKB:  Q5P5I1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P5I1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT214Aromatoleum aromaticum EbN1Mutation(s): 0 
EC: 1.17.99.2
UniProt
Find proteins for Q5P5I2 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1))
Explore Q5P5I2 
Go to UniProtKB:  Q5P5I2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5P5I2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MD1

Query on MD1



Download:Ideal Coordinates CCD File
N [auth A]PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
C20 H26 N10 O13 P2 S2
IRGDLSAXQOKWLX-XHEYTWMPSA-N
MGD

Query on MGD



Download:Ideal Coordinates CCD File
M [auth A]2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
X [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4

Query on SF4



Download:Ideal Coordinates CCD File
K [auth A],
S [auth B],
T [auth B],
U [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
R [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
MO

Query on MO



Download:Ideal Coordinates CCD File
L [auth A]MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
P [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
O [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
O [auth B],
Q [auth B],
V [auth C],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.183 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.532α = 90
b = 67.324β = 111.3
c = 114.765γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other