6NA6

Serial Femtosecond X-ray Crystallography Structure of ECR in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb6NA6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Kitasatospora setae KM-6054
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-05 Released: 2019-12-11 
• Deposition Author(s): DeMirci, H.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.333 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Literature

Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

DeMirci, H., Rao, Y., Stoffel, G.M., Vogeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R.G., Hunter, M.S., Dao, E.H., Ciftci, H.I., Hayes, B., Poitevin, F., Li, P.N., Kaur, M., Tono, K., Saez, D.A., Deutsch, S., Yoshikuni, Y., Grubmuller, H., Erb, T.J., Vohringer-Martinez, E., Wakatsuki, S.

(2022) ACS Cent Sci 

• DOI: https://doi.org/10.1021/acscentsci.2c00057

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 198.27 kDa 
• Atom Count: 14,569 
• Modelled Residue Count: 1,780 
• Deposited Residue Count: 1,780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative crotonyl-CoA reductase	A, B, C [auth D], D [auth C]	445	Kitasatospora setae KM-6054	Mutation(s): 0  Gene Names: ccr1, KSE_56510
UniProt
Find proteins for E4N096 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)) Explore E4N096  Go to UniProtKB:  E4N096

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], F [auth B], G [auth D], H [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.333 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.76	α = 90
b = 78.05	β = 107.76
c = 138	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): DeMirci, H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-1231306

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2020-04-29
  Changes: Data collection
• Version 1.2: 2022-05-11
  Changes: Advisory, Database references
• Version 1.3: 2024-05-22
  Changes: Data collection