3WJC

Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently linked with [Rh(Cp-Mal)(COD)] (NB4-Rh) from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb3WJC/pdb

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


• Deposited: 2013-10-08 Released: 2014-04-09 
• Deposition Author(s): Mizohata, E., Fukumoto, K., Onoda, A., Bocola, M., Arlt, M., Inoue, T., Schwaneberg, U., Hayashi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.295 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Literature

A Rhodium Complex-linked Hybrid Biocatalyst: Stereo-controlled Phenylacetylene Polymerization within an Engineered Protein Cavity

Fukumoto, K., Onoda, A., Mizohata, E., Bocola, M., Inoue, T., Schwaneberg, U., Hayashi, T.

(2014) ChemCatChem 

• DOI: https://doi.org/10.1002/cctc.201301055

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: 40.23 kDa 
• Atom Count: 2,616 
• Modelled Residue Count: 306 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0678 fatty acid-binding protein-like protein At1g79260	A, B	174	Arabidopsis thaliana	Mutation(s): 5  Gene Names: At1g79260, At1g79260.1, 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
RMD	C [auth A], F [auth B]	[(1,2,5,6-eta)-cyclooctane-1,2,5,6-tetrayl]{(1,2,3,4,5-eta)-1-[2-(2,5-dioxopyrrolidin-1-yl)ethyl]cyclopentadienyl}rhodium C19 H24 N O2 Rh SZAWNSHHLUVDRC-UHFFFAOYSA-N
BA	D [auth A], E [auth A], G [auth B], H [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.295 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.888	α = 90
b = 67.888	β = 90
c = 129.895	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Mizohata, E., Fukumoto, K., Onoda, A., Bocola, M., Arlt, M., Inoue, T., Schwaneberg, U., Hayashi, T.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release