1Y0G | pdb_00001y0g

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI YCEI PROTEIN, STRUCTURAL GENOMICS

• PDB DOI: https://doi.org/10.2210/pdb1Y0G/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2004-11-15 Released: 2004-12-21 
• Deposition Author(s): Patskovsky, Y.V., Strokopytov, B., Ramagopal, U., Almo, S.C., 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: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI YCEI PERIPLASMIC PROTEIN

Patskovsky, Y.V., Strokopytov, B., Ramagopal, U., Almo, S.C.

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: 86.31 kDa 
• Atom Count: 5,796 
• Modeled Residue Count: 676 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein yceI	A, B, C, D	191	Escherichia coli	Mutation(s): 0  Gene Names: yceI Membrane Entity: Yes
UniProt
Find proteins for P0A8X2 (Escherichia coli (strain K12)) Explore P0A8X2  Go to UniProtKB:  P0A8X2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8PP	E [auth A], F [auth B], G [auth C], H [auth D]	2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL C46 H70 O VUNQJPPPTJIREN-CMAXTTDKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.17	α = 90
b = 41.93	β = 126.33
c = 130.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BRUTE	model building
CNS	refinement
BRUTE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Patskovsky, Y.V., Strokopytov, B., Ramagopal, U., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2023-08-23
  Changes: Data collection, Database references, Refinement description