4HX0

Crystal structure of a putative nucleotidyltransferase (TM1012) from Thermotoga maritima at 1.87 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of putative nucleotidyltransferase with two MPD molecules in the active site.

Boyko, K.M.Gorbacheva, M.A.Korzhenevskiy, D.A.Lipkin, A.V.Popov, V.O.Kovalchuk, M.V.Shumilin, I.A.Minor, W.Shabalin, I.G.Golubev, A.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative nucleotidyltransferase TM1012163Thermotoga maritimaMutation(s): 0 
Gene Names: TM_1012
UniProt
Find proteins for Q9X0A5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0A5 
Go to UniProtKB:  Q9X0A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0A5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
BU1
Query on BU1

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.196α = 90
b = 52.722β = 105.05
c = 53.508γ = 90
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description