1JZT | pdb_00001jzt

Crystal structure of yeast ynu0, YNL200c

• PDB DOI: https://doi.org/10.2210/pdb1JZT/pdb

• Classification: structural genomics, unknown function
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-09-17 Released: 2001-09-26 
• Deposition Author(s): Jiang, J.-S., Manning, N.O., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal Structure of Yeast Hypothetical Protein YNU0_YEAST

Jiang, J.-S., Manning, N.O., Eswaramoorthy, S., Gerchman, S.E., Kumaran, D., Kycia, J.H., Lewis, H.A., Swaminathan, S., Studier, F.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 55.55 kDa 
• Atom Count: 4,153 
• Modeled Residue Count: 486 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 27.5 kDa protein in SPX19-GCR2 intergenic region	A, B	246	Saccharomyces cerevisiae	Mutation(s): 4  Gene Names: YNL200C EC: 5.1.99.6
UniProt
Find proteins for P40165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40165  Go to UniProtKB:  P40165

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.94 Å
• R-Value Free:  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.732	α = 90
b = 68.676	β = 90
c = 125.187	γ = 90

Software Package:

Software Name	Purpose
ARP/wARP	model building
SOLVE	phasing
CNS	refinement
CCP4	model building
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-26 
Deposition Author(s): Jiang, J.-S., Manning, N.O., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2001-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-11-26
  Changes: Other
• Version 1.4: 2021-02-03
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-06
  Changes: Advisory, Data collection, Database references, Structure summary