2OGF | pdb_00002ogf

Crystal structure of protein MJ0408 from Methanococcus jannaschii, Pfam DUF372

• PDB DOI: https://doi.org/10.2210/pdb2OGF/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-05 Released: 2007-01-16 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hypothetical protein MJ0408 from Methanococcus jannaschii

Ramagopal, U.A., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 58.69 kDa 
• Atom Count: 4,488 
• Modeled Residue Count: 486 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein MJ0408	A, B, C, D	122	Methanocaldococcus jannaschii	Mutation(s): 3  Gene Names: MJ0408 EC: 4.1.2.25
UniProt
Find proteins for Q57851 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57851  Go to UniProtKB:  Q57851

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXG	E [auth A], F [auth A], H [auth B], L [auth D]	8-OXOGUANINE C5 H3 N5 O2 UBKVUFQGVWHZIR-UHFFFAOYSA-N
SO4	G [auth B], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth C], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.693	α = 90
b = 46.27	β = 118.54
c = 79.276	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Ramagopal, U.A., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2023-11-15
  Changes: Data collection
• Version 1.8: 2024-11-13
  Changes: Structure summary