4HX0 | pdb_00004hx0

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

• PDB DOI: https://doi.org/10.2210/pdb4HX0/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-09 Released: 2013-09-11 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.09 kDa 
• Atom Count: 1,762 
• Modeled Residue Count: 161 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nucleotidyltransferase TM1012	A	163	Thermotoga maritima	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	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	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	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 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.196	α = 90
b = 52.722	β = 105.05
c = 53.508	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): 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.

Revision History  

• 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