1X87 | pdb_00001x87

2.4A X-ray structure of Urocanase protein complexed with NAD

• PDB DOI: https://doi.org/10.2210/pdb1X87/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-17 Released: 2004-10-05 
• Deposition Author(s): Tereshko, V., Zaborske, J., Gilbreth, R., Dementieva, I., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

2.4A X-ray structure of Urocanase protein complexed with NAD

Tereshko, V., Zaborske, J., Gilbreth, R., Dementieva, I., Collart, F., Joachimiak, A., Kossiakoff, A.

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: 123.29 kDa 
• Atom Count: 7,883 
• Modeled Residue Count: 988 
• Deposited Residue Count: 1,102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urocanase protein	A, B	551	Geobacillus stearothermophilus	Mutation(s): 0  EC: 4.2.1.49
UniProt
Find proteins for Q5L084 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L084  Go to UniProtKB:  Q5L084

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.118	α = 90
b = 101.614	β = 90
c = 113.854	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Tereshko, V., Zaborske, J., Gilbreth, R., Dementieva, I., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary