6P8C | pdb_00006p8c

2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

• PDB DOI: https://doi.org/10.2210/pdb6P8C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-06 Released: 2020-06-10 
• Deposition Author(s): Carbone, V., Schofield, L.R., Hannus, I., Sutherland-Smith, A.J., Ronimus, R.S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.222 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus

Carbone, V., Schofield, L.R., Hannus, I., Sutherland-Smith, A.J., Ronimus, R.S.

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.

Macromolecule Content 

• Total Structure Weight: 56.75 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 432 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase	A, B	249	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: MTH_235 EC: 1.1.1.302
UniProt
Find proteins for O26337 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26337  Go to UniProtKB:  O26337

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.222 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.921	α = 90
b = 89.597	β = 90
c = 107.013	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Carbone, V., Schofield, L.R., Hannus, I., Sutherland-Smith, A.J., Ronimus, R.S.

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Funding Organization	Location	Grant Number
Other government	New Zealand	--

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description