3L0Z

Crystal structure of a putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Methanocaldococcus jannaschii DSM 2661

• PDB DOI: https://doi.org/10.2210/pdb3L0Z/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-12-10 Released: 2010-01-26 
• Deposition Author(s): Nocek, B., Hatzos, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.262 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Crystal structure of a putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Methanocaldococcus jannaschii DSM 2661

Nocek, B., Hatzos, C., Clancy, S., Joachimiak, A.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.05 kDa 
• Atom Count: 7,656 
• Modelled Residue Count: 1,028 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase	A, B, C	350	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ1598
UniProt
Find proteins for Q58993 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58993  Go to UniProtKB:  Q58993

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth C], J [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 2.65 Å
• R-Value Free: 0.262 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.305	α = 90
b = 119.305	β = 90
c = 170.105	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
MLPHARE	phasing
Coot	model building
RESOLVE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Nocek, B., Hatzos, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary