6VPU

1.90 Angstrom Resolution Crystal Structure Phosphoadenosine Phosphosulfate Reductase (CysH) from Vibrio vulnificus

• PDB DOI: https://doi.org/10.2210/pdb6VPU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-04 Released: 2021-02-10 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Wiersum, G., Endres, M., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

1.90 Angstrom Resolution Crystal Structure Phosphoadenosine Phosphosulfate Reductase (CysH) from Vibrio vulnificus

Minasov, G., Shuvalova, L., Dubrovska, I., Wiersum, G., Endres, M., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Biological Assembly 9  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 9 generated by PISA (software)

Biological Assembly 10  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 10 generated by PISA (software)

Biological Assembly 11  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 11 generated by PISA (software)

Biological Assembly 12  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 12 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 238.6 kDa 
• Atom Count: 16,978 
• Modelled Residue Count: 1,801 
• Deposited Residue Count: 2,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoadenosine phosphosulfate reductase	A, B, C, D, E, F, G, H	261	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: cysH, VV1_1404 EC: 1.8.4.8
UniProt
Find proteins for Q8CWK6 (Vibrio vulnificus (strain CMCP6)) Explore Q8CWK6  Go to UniProtKB:  Q8CWK6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	K [auth D]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	J [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36vpu

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.758	α = 90
b = 76.637	β = 102.89
c = 143.876	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Currently 6VPU does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Wiersum, G., Endres, M., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description