5B53 | pdb_00005b53

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum

• PDB DOI: https://doi.org/10.2210/pdb5B53/pdb

• Classification: TRANSFERASE
• Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-22 Released: 2017-04-26 
• Deposition Author(s): Kezuka, Y., Yoshida, Y., Nonaka, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum

Kezuka, Y., Yoshida, Y., Nonaka, T.

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)

Macromolecule Content 

• Total Structure Weight: 37.87 kDa 
• Atom Count: 2,624 
• Modeled Residue Count: 334 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A	340	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0  Gene Names: FN1055 EC: 2.5.1.47
UniProt
Find proteins for Q8REP3 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8REP3  Go to UniProtKB:  Q8REP3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.793	α = 90
b = 58.793	β = 90
c = 205.053	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Kezuka, Y., Yoshida, Y., Nonaka, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	21791810
Japan Society for the Promotion of Science	Japan	23792130

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description