2EFV | pdb_00002efv

Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb2EFV/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-26 Released: 2007-08-28 
• Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold

Thiruselvam, V., Kumarevel, T., Karthe, P., Kuramitsu, S., Yokoyama, S., Ponnuswamy, M.N.

(2017) Biochem Biophys Res Commun 482: 264-269

• PubMed: 27845039 
• DOI: https://doi.org/10.1016/j.bbrc.2016.11.052
• Primary Citation of Related Structures:  
  2EFV


• PubMed Abstract: 
  

  The crystal structure of a hypothetical protein MJ0366, derived from Methanocaldococcus jannaschii was solved at 1.9 Å resolution using synchrotron radiation. MJ0366 was crystallized as a monomer and has knot structural arrangement. Intriguingly, the solved structure consists of novel 'KNOT' fold conformation. The 3 ₁ trefoil knot was observed in the structure. The N-terminal and C-terminal ends did not participate in knot formation.

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Organizational Affiliation: 

Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.97 kDa 
• Atom Count: 762 
• Modelled Residue Count: 82 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein MJ0366	A	92	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: mj0366
UniProt
Find proteins for Q57812 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57812  Go to UniProtKB:  Q57812

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.846	α = 90
b = 78.846	β = 90
c = 35.104	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-01-16
  Changes: Data collection, Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations