2FKN | pdb_00002fkn

crystal structure of urocanase from bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2FKN/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-05 Released: 2007-01-02 
• Deposition Author(s): Yu, Y.-M., Liang, Y.-H., Su, X.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal Structure of Urocanase from Bacillus Subtilis

Yu, Y.-M., Liang, Y.-H., Su, X.-D.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 245.6 kDa 
• Atom Count: 17,568 
• Modeled Residue Count: 2,178 
• Deposited Residue Count: 2,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urocanate hydratase	A, B, C, D	552	Bacillus subtilis	Mutation(s): 0  Gene Names: hutU EC: 4.2.1.49
UniProt
Find proteins for P25503 (Bacillus subtilis (strain 168)) Explore P25503  Go to UniProtKB:  P25503

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], H [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ACT	E [auth A], G [auth B], I [auth C], K [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.791	α = 90
b = 131.268	β = 90
c = 164.696	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
HLK	data reduction
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Yu, Y.-M., Liang, Y.-H., Su, X.-D.

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-12
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations