5VYV | pdb_00005vyv

Crystal structure of a protein of unknown function YceH/ECK1052 involved in membrane biogenesis from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb5VYV/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-26 Released: 2017-06-07 
• Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a protein of unknown function YceH/ECK1052 involved in membrane biogenesis from Escherichia coli

Stogios, P.J.

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: 48.51 kDa 
• Atom Count: 2,882 
• Modeled Residue Count: 343 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0502 protein YceH	A, B	215	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: yceH, Z1704, ECs1445
UniProt
Find proteins for P29217 (Escherichia coli (strain K12)) Explore P29217  Go to UniProtKB:  P29217

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35vyv

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.777	α = 90
b = 74.853	β = 100.73
c = 58.661	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description