3C18

Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from Exiguobacterium sibiricum 255-15 at 1.90 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb3C18/pdb

• Classification: TRANSFERASE
• Organism(s): Exiguobacterium sibiricum 255-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-22 Released: 2008-02-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from Exiguobacterium sibiricum 255-15 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 103.75 kDa 
• Atom Count: 7,811 
• Modelled Residue Count: 869 
• Deposited Residue Count: 870 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyltransferase-like protein	A, B, C	290	Exiguobacterium sibiricum 255-15	Mutation(s): 0  Gene Names: ZP_00538802.1, ExigDRAFT_1952, Exig_0661
UniProt
Find proteins for B1YK61 (Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YK61  Go to UniProtKB:  B1YK61

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth B], I [auth C], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.233 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M33C18

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.74	α = 90
b = 66.74	β = 90
c = 456.2	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations