4YMY | pdb_00004ymy

Crystal structure of mutant nitrobindin M75A/H76L/Q96C/M148L/H158A (NB11) from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4YMY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-08 Released: 2015-12-30 
• Deposition Author(s): Mizohata, E., Himiyama, T., Tachikawa, K., Oohora, K., Onoda, A., Hayashi, T.
• Funding Organization(s): MEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.136 (Depositor), 0.137 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

Literature

A Highly Active Biohybrid Catalyst for Olefin Metathesis in Water: Impact of a Hydrophobic Cavity in a beta-Barrel Protein

Sauer, D.F., Himiyama, T., Tachikawa, K., Fukumoto, K., Onoda, A., Mizohata, E., Inoue, T., Bocola, M., Schwaneberg, U., Hayashi, T., Okuda, J.

(2015) ACS Catal 5: 7519-7522

• DOI: https://doi.org/10.1021/acscatal.5b01792

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: 19.72 kDa 
• Atom Count: 1,479 
• Modeled Residue Count: 153 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0678 fatty acid-binding protein-like protein At1g79260	A	174	Arabidopsis thaliana	Mutation(s): 5  Gene Names: At1g79260, YUP8H12R.14 EC: 5.99
UniProt
Find proteins for O64527 (Arabidopsis thaliana) Explore O64527  Go to UniProtKB:  O64527

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.136 (Depositor), 0.137 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.654	α = 90
b = 79.285	β = 90
c = 36.409	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
PHASER	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Mizohata, E., Himiyama, T., Tachikawa, K., Oohora, K., Onoda, A., Hayashi, T.

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Funding Organization	Location	Grant Number
MEXT	Japan	area 2204

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description