7ROM | pdb_00007rom

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

  • 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)

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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-cytochrome b5 reductase 1261Saccharomyces cerevisiaeMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38626
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD
Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PGE
Query on PGE
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
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 = 72.225α = 90
b = 72.225β = 90
c = 114.669γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK107868-04
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124165-01
National Institutes of Health/Office of the DirectorUnited StatesS10OD021527
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

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