8P3M

The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals

Varfolomeeva, L.A.Polyakov, K.M.Komolov, A.S.Rakitina, T.V.Dergousova, N.I.Dorovatovskii, P.V.Boyko, K.M.Tikhonova, T.V.Popov, V.O.

(2023) Crystallogr Rep 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Twin-arginine translocation signal domain-containing protein494Thioalkalivibrio paradoxus ARh 1Mutation(s): 1 
Gene Names: THITH_13335
UniProt
Find proteins for W0DP94 (Thioalkalivibrio paradoxus ARh 1)
Explore W0DP94 
Go to UniProtKB:  W0DP94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0DP94
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth 5]
CA [auth J]
DB [auth 8]
FA [auth M]
GB [auth x]
AB [auth 5],
CA [auth J],
DB [auth 8],
FA [auth M],
GB [auth x],
IA [auth P],
JA [auth P],
LB [auth h],
NA [auth S],
OB [auth k],
Q [auth A],
QA [auth V],
U [auth A],
UA [auth Y],
V [auth D],
XA [auth 2],
Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
BB [auth 5]
CB [auth 5]
DA [auth J]
AA [auth G],
BA [auth G],
BB [auth 5],
CB [auth 5],
DA [auth J],
EA [auth J],
EB [auth 8],
FB [auth 8],
GA [auth M],
HA [auth M],
HB [auth x],
IB [auth x],
JB [auth e],
KA [auth P],
KB [auth e],
LA [auth P],
MB [auth h],
NB [auth h],
OA [auth S],
PA [auth S],
PB [auth k],
QB [auth k],
RA [auth V],
S [auth A],
SA [auth V],
T [auth A],
VA [auth Y],
WA [auth Y],
X [auth D],
Y [auth D],
YA [auth 2],
ZA [auth 2]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
BO3
Query on BO3

Download Ideal Coordinates CCD File 
R [auth A],
W [auth D]
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
MA [auth P],
TA [auth V]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.15α = 90
b = 142.42β = 90.07
c = 294.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation23-74-30004

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references