5UHJ | pdb_00005uhj

The crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234

• PDB DOI: https://doi.org/10.2210/pdb5UHJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces sp. CB03234
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-11 Released: 2017-01-25 
• Deposition Author(s): Tan, K., Li, H., Endres, M., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• 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: 1.75 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The crystal structure of a natural product biosynthetic enzyme from Streptomyces sp. CB03234

Tan, K., Li, H., Endres, M., Phillips Jr., G.N., Joachimiak, A.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.39 kDa 
• Atom Count: 2,051 
• Modeled Residue Count: 245 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resisance protein/dioxygenase	A, B	129	Streptomyces sp. CB03234	Mutation(s): 0  Gene Names: tnmS1
UniProt
Find proteins for A0A125SA24 (Streptomyces sp. (strain CB03234)) Explore A0A125SA24  Go to UniProtKB:  A0A125SA24

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.836	α = 90
b = 33.346	β = 98.49
c = 101.781	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Tan, K., Li, H., Endres, M., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2020-09-23
  Changes: Database references, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary