7DNN | pdb_00007dnn

Crystal structure of the AgCarB2-C2 complex with homoorientin

• PDB DOI: https://doi.org/10.2210/pdb7DNN/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Arthrobacter globiformis NBRC 12137
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-10 Released: 2021-10-20 
• Deposition Author(s): Senda, M., Kumano, T., Watanabe, S., Kobayashi, M., Senda, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria

Mori, T., Kumano, T., He, K., Awakawa, T., Watanabe, S., Hori, S., Terashita, Y., Hashimoto, Y., Senda, M., Senda, T., Kobayashi, M., Abe, I.

(2021) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 114.39 kDa 
• Atom Count: 7,526 
• Modeled Residue Count: 934 
• Deposited Residue Count: 998 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP_endonuc_2 domain-containing protein	A, C [auth P]	354	Arthrobacter globiformis NBRC 12137	Mutation(s): 0  Gene Names: ARGLB_075_00530 EC: 4.1.99
UniProt
Find proteins for H0QPL9 (Arthrobacter globiformis (strain ATCC 8010 / DSM 20124 / JCM 1332 / NBRC 12137 / NCIMB 8907 / NRRL B-2979 / 168)) Explore H0QPL9  Go to UniProtKB:  H0QPL9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AgCarC2	B, D [auth Q]	145	Arthrobacter globiformis NBRC 12137	Mutation(s): 0  Gene Names: ARGLB_075_00520 EC: 4.1.99
UniProt
Find proteins for H0QPL8 (Arthrobacter globiformis (strain ATCC 8010 / DSM 20124 / JCM 1332 / NBRC 12137 / NCIMB 8907 / NRRL B-2979 / 168)) Explore H0QPL8  Go to UniProtKB:  H0QPL8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H9R (Subject of Investigation/LOI)	E [auth A]	2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one C21 H20 O11 ODBRNZZJSYPIDI-VJXVFPJBSA-N
IOD	G [auth A], I [auth P]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
MN (Subject of Investigation/LOI)	F [auth A], H [auth P]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.905	α = 90
b = 102.511	β = 90
c = 136.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Senda, M., Kumano, T., Watanabe, S., Kobayashi, M., Senda, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101001

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection