2AVN | pdb_00002avn

CRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN (TM1389) FROM THERMOTOGA MARITIMA MSB8 AT 2.35 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2AVN/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-30 Released: 2005-10-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.179 (DCC) 

Literature

Crystal structure of Ubiquinone/menaquinone biosynthesis methyltransferase-related protein (tm1389) from THERMOTOGA MARITIMA at 2.35 A resolution

Joint Center for Structural Genomics (JCSG)

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 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.14 kDa 
• Atom Count: 4,279 
• Modeled Residue Count: 494 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquinone/menaquinone biosynthesis methyltransferase-related protein	A, B	260	Thermotoga maritima MSB8	Mutation(s): 6  Gene Names: tm1389
UniProt
Find proteins for Q9X1A9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1A9  Go to UniProtKB:  Q9X1A9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAI	D [auth A], E [auth B]	S-ADENOSYL-L-HOMOSELENOCYSTEINE C14 H20 N6 O5 Se UVSMMLABJBJNGH-WFMPWKQPSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.179 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32AVN

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.475	α = 90
b = 130.475	β = 90
c = 192.926	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-10-18
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary