Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.41 kDa 
• Atom Count: 2015 
• Modelled Residue Count: 230 
• Deposited Residue Count: 257 
• Unique protein chains: 1

1B54

CRYSTAL STRUCTURE OF A YEAST HYPOTHETICAL PROTEIN-A STRUCTURE FROM BNL'S HUMAN PROTEOME PROJECT

• DOI: 10.2210/pdb1B54/pdb

• Classification: HYPOTHETICAL PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-01-12 Released: 1999-01-27 
• Deposition Author(s): Swaminathan, S., Eswaramoorthy, 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: 2.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 

Literature

Structure of a yeast hypothetical protein selected by a structural genomics approach.

Eswaramoorthy, S., Gerchman, S., Graziano, V., Kycia, H., Studier, F.W., Swaminathan, S.

(2003) Acta Crystallogr D Biol Crystallogr 59: 127-135

• PubMed: 12499548 
• DOI: 10.1107/s0907444902018012
• Primary Citation of Related Structures:  
  1CT5, 1B54


• PubMed Abstract: 
  

Yeast hypothetical protein YBL036C (SWISS-PROT P38197), initially thought to be a member of an 11-protein family, was selected for crystal structure determination since no structural or functional information was available. The structure has been determined independently by MIR and MAD methods to 2.0 A resolution. The MAD structure was determined largely through automated model building. The protein folds as a TIM barrel beginning with a long N-terminal helix, in contrast to the classic triose phosphate isomerase (TIM) structure, which begins with a beta-strand. A cofactor, pyridoxal 5'-phosphate, is covalently bound near the C-terminal end of the barrel, the usual active site in TIM-barrel folds. A single-domain monomeric molecule, this yeast protein resembles the N-terminal domain of alanine racemase or ornithine decarboxylase, both of which are two-domain dimeric proteins. The yeast protein has been shown to have amino-acid racemase activity. Although selected as a member of a protein family having no obvious relationship to proteins of known structure, the protein fold turned out to be a well known and widely distributed fold. This points to the need for a more comprehensive base of structural information and better structure-modeling tools before the goal of structure prediction from amino-acid sequences can be realised. In this case, similarity to a known structure allowed inferences to be made about the structure and function of a widely distributed protein family.

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Organizational Affiliation: 

Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEAST HYPOTHETICAL PROTEIN	A	257	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SGD: YBL 036C
UniProt
Find proteins for P38197 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38197  Go to UniProtKB:  P38197

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.303 
• R-Value Work: 0.235 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.58	α = 90
b = 65.71	β = 90
c = 91.94	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 1999-01-12 
• Released Date: 1999-01-27 
Deposition Author(s): Swaminathan, S., Eswaramoorthy, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 1999-01-27
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Derived calculations, Structure summary