8I29 | pdb_00008i29

Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb8I29/pdb
• Entry: 8I29 supersedes: 7YIP

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2023-01-14 Released: 2023-02-01 
• Deposition Author(s): Bai, X., Lan, J., Bu, T.T., Wang, L.L., He, S.R., Zhang, J., Xu, Y.B.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum

Bai, X., Lan, J., Bu, T.T., He, S.R., Zhang, J., Wang, L.L.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.19 kDa 
• Atom Count: 3,121 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.426	α = 90
b = 79.351	β = 90
c = 212.932	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Bai, X., Lan, J., Bu, T.T., Wang, L.L., He, S.R., Zhang, J., Xu, Y.B.
• This entry supersedes: 7YIP

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection