3WJD

Crystal structure of mutant nitrobindin F44W/M75L/H76L/Q96C/M148L/H158L (NB5) from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb3WJD/pdb

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

Deposited: 2013-10-08 Released: 2014-04-02
Deposition Author(s): Mizohata, E., Fukumoto, K., Onoda, A., Bocola, M., Arlt, M., Inoue, T., Schwaneberg, U., Hayashi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.166
R-Value Work: 0.145
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 19.57 kDa
Atom Count: 1,471
Modelled Residue Count: 153
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0678 fatty acid-binding protein-like protein At1g79260	A	174	Arabidopsis thaliana	Mutation(s): 6 Gene Names: At1g79260, At1g79260.1, YUP8H12R.14
UniProt
Find proteins for O64527 (Arabidopsis thaliana) Explore O64527 Go to UniProtKB: O64527
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O64527
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.166
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.849	α = 90
b = 79.419	β = 90
c = 36.329	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Schwaneberg, U.

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.