3WJD | pdb_00003wjd

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 (Depositor), 0.165 (DCC)
R-Value Work:
0.145 (Depositor), 0.144 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3WJD

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
Modeled Residue Count: 153
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 EC: 5.99
UniProt
Find proteins for O64527 (Arabidopsis thaliana) Explore O64527 Go to UniProtKB: O64527
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.165 (DCC)
R-Value Work: 0.145 (Depositor), 0.144 (DCC)
R-Value Observed: 0.146 (Depositor)

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

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View more in-depth experimental data

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.