5VIS | pdb_00005vis

1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.

• PDB DOI: https://doi.org/10.2210/pdb5VIS/pdb

• Classification: HYDROLASE,OXIDOREDUCTASE
• Organism(s): soil metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-17 Released: 2017-05-03 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Di Leo, R., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.

Minasov, G., Wawrzak, Z., Di Leo, R., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.87 kDa 
• Atom Count: 5,027 
• Modeled Residue Count: 542 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate Synthase	A, B	275	soil metagenome	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	F [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
MLA	C [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35vis

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.822	α = 90
b = 101.822	β = 90
c = 206.137	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Minasov, G., Wawrzak, Z., Di Leo, R., Skarina, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2018-10-17
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-04-03
  Changes: Data collection, Other, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description