5W27 | pdb_00005w27

Crystal structure of TnmS3 in complex with tiancimycin (TNM B)

• PDB DOI: https://doi.org/10.2210/pdb5W27/pdb

• Classification: Tiancimycin-binding protein
• Organism(s): Streptomyces sp. CB03234
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-05 Released: 2018-06-06 
• Deposition Author(s): Chang, C.Y., Chang, C., Nocek, B., Rudolf, J.D., Joachimiak, A., Phillips Jr., G.N., SHen, B., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TnmS3 in complex with tiancimycin (TNM B)

Chang, C.Y., Chang, C., Nocek, B., Rudolf, J.D., Joachimiak, A., Phillips, G.N., SHen, B., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.02 kDa 
• Atom Count: 2,167 
• Modeled Residue Count: 242 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resisance protein/dioxygenase	A, B	144	Streptomyces sp. CB03234	Mutation(s): 0  Gene Names: tnmS3, AMK26_32110
UniProt
Find proteins for A0A125SA29 (Streptomyces sp. (strain CB03234)) Explore A0A125SA29  Go to UniProtKB:  A0A125SA29

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9VG	C [auth A], D [auth B]	methyl (2E)-3-[(1aS,11S,11aS,14Z,18R)-3,18-dihydroxy-4,9-dioxo-4,9,10,11-tetrahydro-11aH-11,1a-hept[3]ene[1,5]diynonaphtho[2,3-h]oxireno[c]quinolin-11a-yl]but-2-enoate C29 H19 N O7 VNWTWPJYWHYMNF-PUHZCEAISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.576	α = 90
b = 67.698	β = 90
c = 84.323	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Chang, C.Y., Chang, C., Nocek, B., Rudolf, J.D., Joachimiak, A., Phillips Jr., G.N., SHen, B., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description