7ROM | pdb_00007rom

Crystal structure of Saccharomyces cerevisiae NADH-cytochrome b5 reductase 1 (Cbr1) fragment (residues 28-284) bound to FAD

• PDB DOI: https://doi.org/10.2210/pdb7ROM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-31 Released: 2022-08-10 
• Deposition Author(s): Fenwick, M.K., Zhang, Y., Lin, H.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Saccharomyces cerevisiae NADH-cytochrome b5 reductase 1 (Cbr1) fragment (residues 28-284) bound to FAD

Fenwick, M.K., Lin, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 30.22 kDa 
• Atom Count: 2,635 
• Modeled Residue Count: 255 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-cytochrome b5 reductase 1	A	261	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CBR1, CBR, CBR5, YIL043C EC: 1.6.2.2
UniProt
Find proteins for P38626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38626  Go to UniProtKB:  P38626

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PGE	F [auth A], G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.225	α = 90
b = 72.225	β = 90
c = 114.669	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Fenwick, M.K., Zhang, Y., Lin, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK107868-04
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165-01
National Institutes of Health/Office of the Director	United States	S10OD021527
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description