3OWM

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase

Trofimov, A.A.Polyakov, K.M.Tikhonova, T.V.Popov, V.O.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eight-heme nitrite reductase
A, B
519Thioalkalivibrio nitratireducensMutation(s): 0 
EC: 1.7.2.2
UniProt
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Explore L0DSL2 
Go to UniProtKB:  L0DSL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0DSL2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
J [auth A],
Z [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6
Query on PG6

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MA [auth B]
NA [auth B]
P [auth A]
PA [auth B]
QA [auth B]
MA [auth B],
NA [auth B],
P [auth A],
PA [auth B],
QA [auth B],
R [auth A],
S [auth A]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4

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OA [auth B]
Q [auth A]
RA [auth B]
SA [auth B]
T [auth A]
OA [auth B],
Q [auth A],
RA [auth B],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
X [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS
Query on TRS

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KA [auth B],
N [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
NO2
Query on NO2

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HA [auth B],
K [auth A]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
CA
Query on CA

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IA [auth B]
JA [auth B]
L [auth A]
LA [auth B]
M [auth A]
IA [auth B],
JA [auth B],
L [auth A],
LA [auth B],
M [auth A],
O [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

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Y [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.529α = 90
b = 192.529β = 90
c = 192.529γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description