7BBM

Mutant nitrobindin M75L/H76L/Q96C/M148L (NB4H) from Arabidopsis thaliana with cofactor MnPPIX

• PDB DOI: https://doi.org/10.2210/pdb7BBM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-18 Released: 2021-05-26 
• Deposition Author(s): Minges, A., Sauer, D.F., Wittwer, M., Markel, U., Spiertz, M., Schiffels, J., Davari, M.D., Okuda, J., Schwaneberg, U., Groth, G.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.158 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 

Literature

Chemogenetic engineering of nitrobindin toward an artificial epoxygenase

Sauer, D.F., Wittwer, M., Markel, U., Minges, A., Spiertz, M., Schiffels, J., Davari, M.D., Groth, G., Okuda, J., Schwaneberg, U.

(2021) Catal Sci Technol 

• DOI: https://doi.org/10.1039/d1cy00609f

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 19.41 kDa 
• Atom Count: 1,620 
• Modelled Residue Count: 153 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0678 fatty acid-binding protein-like protein At1g79260	A	166	Arabidopsis thaliana	Mutation(s): 4  Gene Names: At1g79260, YUP8H12R.14
UniProt
Find proteins for O64527 (Arabidopsis thaliana) Explore O64527  Go to UniProtKB:  O64527

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNH (Subject of Investigation/LOI)	H [auth A]	MANGANESE PROTOPORPHYRIN IX C34 H32 Mn N4 O4 UIBYYPDLEONCGQ-RGGAHWMASA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.158 
• R-Value Work: 0.144 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.5281/zenodo.4277282

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.9	α = 90
b = 79.547	β = 90
c = 36.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
BUCCANEER	model building
PHASER	phasing
Aimless	data scaling
XDS	data reduction
MxCuBE	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Minges, A., Sauer, D.F., Wittwer, M., Markel, U., Spiertz, M., Schiffels, J., Davari, M.D., Okuda, J., Schwaneberg, U., Groth, G.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031B0297

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description