5YOG | pdb_00005yog

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 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

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.
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Insititute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China.
Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, China.
Complex Systems Division, Beijing Computational Science Research Center, Beijing, 100193, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].
iHuman Institute, ShanghaiTech University, Shanghai, 201210, China. [e-mail].
Insititute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, 650500, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. [e-mail].

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 
• Modeled 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 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

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