6L1K

Crystal structure of NADH-dependent butanol dehydrogenase A from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb6L1K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-29 Released: 2019-10-16
Deposition Author(s): Lan, J., Shang, F., Liu, W., Xu, Y., Chen, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of NADH-dependent butanol dehydrogenase A from Fusobacterium nucleatum

Lan, J., Shang, F., Liu, W., Xu, Y., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 43.43 kDa
Atom Count: 3,342
Modelled Residue Count: 384
Deposited Residue Count: 385
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent butanol dehydrogenase A	A	385	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: FN1415 EC: 1.1.1
UniProt
Find proteins for Q8R612 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8R612 Go to UniProtKB: Q8R612
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8R612
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.773	α = 90
b = 78.846	β = 90
c = 215.218	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-10-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History (Full details and data files)

Version 1.0: 2019-10-16
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.