4X4J | pdb_00004x4j

Structural and Functional Studies of BexE: Insights into Oxidation During BE-7585A Biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb4X4J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis orientalis subsp. vinearia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-02 Released: 2015-12-02 
• Deposition Author(s): Tsai, S.-C., Jackson, D.R., Patel, A., Barajas, J.F., Rohr, J., Yu, X., Liu, H.-W., Sasaki, E., Calveras, J., Metsa-Ketela, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Studies of BexE: Insights into Oxidation During BE-7585A Biosynthesis

Tsai, S.-C., Jackson, D.R., Patel, A., Barajas, J.F., Rohr, J., Yu, X., Liu, H.-W., Sasaki, E., Calveras, J., Metsa-Ketela, M.

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)

Macromolecule Content 

• Total Structure Weight: 109.19 kDa 
• Atom Count: 7,341 
• Modeled Residue Count: 962 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxygenase	A, B	507	Amycolatopsis orientalis subsp. vinearia	Mutation(s): 0  Gene Names: bexE
UniProt
Find proteins for D7RFJ3 (Amycolatopsis orientalis subsp. vinearia) Explore D7RFJ3  Go to UniProtKB:  D7RFJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.672	α = 90
b = 80.379	β = 126.19
c = 105.079	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Tsai, S.-C., Jackson, D.R., Patel, A., Barajas, J.F., Rohr, J., Yu, X., Liu, H.-W., Sasaki, E., Calveras, J., Metsa-Ketela, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM100305-03

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description