5L8F | pdb_00005l8f

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A, E62A, H65A.

• PDB DOI: https://doi.org/10.2210/pdb5L8F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-06-07 Released: 2017-06-21 
• Deposition Author(s): He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.
• Funding Organization(s): Chinese Scholarship Council, Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A, E62A, H65A.

He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 132.04 kDa 
• Atom Count: 7,561 
• Modeled Residue Count: 898 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rru_A0973	A, B, C, D, E, F, G, H, I, J	116	Rhodospirillum rubrum ATCC 11170	Mutation(s): 3  Gene Names: Rru_A0973 EC: 1.16.3.1
UniProt
Find proteins for Q2RVS1 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RVS1  Go to UniProtKB:  Q2RVS1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	S [auth G]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MG	K [auth B], L [auth B], M [auth D], N [auth D], O [auth F], P [auth F], Q [auth G], R [auth G], T [auth G], U [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.096	α = 90
b = 92.096	β = 90
c = 217.105	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): He, D., Hughes, S., Vanden-Hehir, S., Georgiev, A., Altenbach, K., Tarrant, E., Mackay, C.L., Waldron, K.J., Clarke, D.J., Marles-Wright, J.

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Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--
Royal Society	United Kingdom	RG130585

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Author supporting evidence, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description