3K32 | pdb_00003k32

The crystal structure of predicted subunit of tRNA methyltransferase from Methanocaldococcus jannaschii DSM

• PDB DOI: https://doi.org/10.2210/pdb3K32/pdb

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


• Deposited: 2009-09-30 Released: 2010-01-12 
• Deposition Author(s): Wu, R., Zhang, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

The crystal structure of predicted subunit of tRNA methyltransferase from Methanocaldococcus jannaschii DSM

Wu, R., Zhang, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.07 kDa 
• Atom Count: 9,636 
• Modeled Residue Count: 1,157 
• Deposited Residue Count: 1,218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ0690	A, B, C, D, E, F	203	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: MJ0690
UniProt
Find proteins for Q58102 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58102  Go to UniProtKB:  Q58102

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B], H [auth C], I [auth E], J [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.669	α = 90
b = 121.951	β = 116.7
c = 81.224	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wu, R., Zhang, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary