1VKM

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.

Levin, I.Miller, M.D.Schwarzenbacher, R.McMullan, D.Abdubek, P.Ambing, E.Biorac, T.Cambell, J.Canaves, J.M.Chiu, H.J.Deacon, A.M.DiDonato, M.Elsliger, M.A.Godzik, A.Grittini, C.Grzechnik, S.K.Hale, J.Hampton, E.Han, G.W.Haugen, J.Hornsby, M.Jaroszewski, L.Karlak, C.Klock, H.E.Koesema, E.Kreusch, A.Kuhn, P.Lesley, S.A.Morse, A.Moy, K.Nigoghossian, E.Ouyang, J.Page, R.Quijano, K.Reyes, R.Robb, A.Sims, E.Spraggon, G.Stevens, R.C.van den Bedem, H.Velasquez, J.Vincent, J.Wang, X.West, B.Wolf, G.Xu, Q.Zagnitko, O.Hodgson, K.O.Wooley, J.Wilson, I.A.

(2005) Proteins 59: 864-868


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
conserved hypothetical protein TM1464
A, B, C, D, E
A, B, C, D, E, F
297Thermotoga maritima MSB8Mutation(s): 10 
Gene Names: TM1464
EC: 4.2.1.70
UniProt
Find proteins for Q9X1H5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1H5 
Go to UniProtKB:  Q9X1H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
GA [auth E]
HA [auth E]
IA [auth E]
AA [auth D],
BA [auth D],
GA [auth E],
HA [auth E],
IA [auth E],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
V [auth C],
W [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
EA [auth E]
G [auth A]
H [auth A]
CA [auth E],
DA [auth E],
EA [auth E],
G [auth A],
H [auth A],
I [auth A],
JA [auth F],
KA [auth F],
L [auth B],
LA [auth F],
M [auth B],
R [auth C],
S [auth C],
T [auth C],
X [auth D],
Y [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
FA [auth E]
J [auth A]
MA [auth F]
N [auth B]
U [auth C]
FA [auth E],
J [auth A],
MA [auth F],
N [auth B],
U [auth C],
Z [auth D]
Unknown ligand
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.958α = 90
b = 130.799β = 90
c = 138.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-01-25
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary