1NKQ | pdb_00001nkq

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein

• PDB DOI: https://doi.org/10.2210/pdb1NKQ/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-03 Released: 2004-06-15 
• Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Daniels, B., Studier, F.W., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.262 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 

Literature

Crtystal Structure of Yeast Hypothetical Protein YNQ8_YEAST

Eswaramoorthy, S., Kumaran, D., Daniels, B., Studier, F.W., Swaminathan, S.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.3 kDa 
• Atom Count: 12,088 
• Modeled Residue Count: 1,466 
• Deposited Residue Count: 1,554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region	A, B, C, D, E, F	259	Saccharomyces cerevisiae	Mutation(s): 6  Gene Names: YNL168C or N1696 EC: 5.3.2.2
UniProt
Find proteins for P53889 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53889  Go to UniProtKB:  P53889

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A], L [auth B], N [auth B], O [auth B], S [auth C], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	AA [auth E], BA [auth E], DA [auth F], EA [auth F], J [auth A], K [auth A], P [auth B], Q [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	CA [auth F], G [auth A], M [auth B], R [auth C], V [auth D], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.705	α = 90
b = 85.99	β = 90
c = 316.704	γ = 90

Software Package:

Software Name	Purpose
MARMAD	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SHARP	phasing
CNS	refinement
MARMAD	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Daniels, B., Studier, F.W., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary