5YOG

Crystal Structure of flavodoxin with engineered disulfide bond N14C-C93

• PDB DOI: https://doi.org/10.2210/pdb5YOG/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-27 Released: 2018-03-14 
• Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.180 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Protein crystal quality oriented disulfide bond engineering.

Pu, M., Xu, Z., Peng, Y., Hou, Y., Liu, D., Wang, Y., Liu, H., Song, G., Liu, Z.J.

(2018) Protein Cell 9: 659-663

• PubMed: 29039033 
• DOI: https://doi.org/10.1007/s13238-017-0482-7
• Primary Citation of Related Structures:  
  5YM7, 5YO3, 5YO4, 5YO5, 5YO6, 5YOB, 5YOC, 5YOE, 5YOG

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.5 kDa 
• Atom Count: 1,352 
• Modelled Residue Count: 148 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin	A	148	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 2  Gene Names: DVU_2680
UniProt
Find proteins for P00323 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00323  Go to UniProtKB:  P00323

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.180 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.607	α = 90
b = 56.321	β = 101.63
c = 41.418	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Pu, M., Xu, Z., Song, G., Liu, Z.J.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary