2EWR | pdb_00002ewr

Crystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2EWR/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-05 Released: 2005-12-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Crystal structure of hypothetical protein (tm1012) from Thermotoga maritima at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.62 kDa 
• Atom Count: 1,563 
• Modeled Residue Count: 156 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1012	A	170	Thermotoga maritima	Mutation(s): 3  Gene Names: tm1012
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32EWR

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.56	α = 74.11
b = 36.21	β = 86.38
c = 39.28	γ = 79.69

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary