6D2V | pdb_00006d2v

Apo Structure of TerB, an NADP Dependent Oxidoreductase in the Terfestatin Biosynthesis Pathway

• PDB DOI: https://doi.org/10.2210/pdb6D2V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-04-14 Released: 2018-06-13 
• Deposition Author(s): Clinger, J.A., Elshahawi, S.I., Zhang, Y., Hall, R.P., Liu, Y., Thorson, J.S., Phillips Jr., G.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Structure and Function of Terfestatin Biosynthesis Enzymes TerB and TerC

Clinger, J.A., Elshahawi, S.I., Zhang, Y., Hall, R.P., Liu, Y., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.65 kDa 
• Atom Count: 5,456 
• Modeled Residue Count: 621 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TerB Oxidoreductase	A, B	315	Streptomyces	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEU0 (Streptomyces) Explore A0A3B6UEU0  Go to UniProtKB:  A0A3B6UEU0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	C [auth A], G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SCN	D [auth A], H [auth B], I [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.516	α = 90
b = 80.598	β = 90
c = 139.518	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Clinger, J.A., Elshahawi, S.I., Zhang, Y., Hall, R.P., Liu, Y., Thorson, J.S., Phillips Jr., G.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Refinement description