1DUS

MJ0882-A hypothetical protein from M. jannaschii

• PDB DOI: https://doi.org/10.2210/pdb1DUS/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-01-18 Released: 2000-07-19 
• Deposition Author(s): Hung, L., Huang, L., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii

Huang, L., Hung, L., Odell, M., Yokota, H., Kim, R., Kim, S.H.

(2002) J Struct Funct Genomics 2: 121-127

• PubMed: 12836702 
• DOI: https://doi.org/10.1023/a:1021279113558
• Primary Citation of Related Structures:  
  1DUS


• PubMed Abstract: 
  

  We have determined the three-dimensional (3-D) structure of protein MJ0882, which derives from a hypothetical open reading frame in the genome of the hyperthermophile Methanococcus jannaschii. The 3-D fold of MJ0882 at 1.8 A highly resembles that of a methyltransferase, despite limited sequence similarity to any confirmed methyltransferase. The structure has an S-adenosylmethionine (AdoMet) binding pocket surrounded by motifs with similarities to those commonly found among AdoMet binding proteins. Preliminary biochemical experiments show that MJ0882 specifically binds to AdoMet, which is the essential co-factor for methyltransferases.

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Organizational Affiliation: 

Dept. of Cellular Biochemistry and Biophysics, Sloan Kettering Institute, 1275 York Ave., New York, NY 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.95 kDa 
• Atom Count: 1,697 
• Modelled Residue Count: 194 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MJ0882	A	194	Methanocaldococcus jannaschii	Mutation(s): 2  EC: 2.1.1
UniProt
Find proteins for Q58292 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58292  Go to UniProtKB:  Q58292

Small Molecules

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: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.34	α = 90
b = 36.78	β = 90
c = 68.34	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-07-19 
Deposition Author(s): Hung, L., Huang, L., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2000-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary