1RC6 | pdb_00001rc6

Crystal structure of protein Ylba from E. coli, Pfam DUF861

• PDB DOI: https://doi.org/10.2210/pdb1RC6/pdb

• Classification: structural genomics, unknown function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-03 Released: 2003-11-18 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Thirumuruhan, R., Ramagopal, U.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of Ylba, hypothetical protein from E.Coli

Fedorov, A.A., Fedorov, E.V., Thirumuruhan, R., Ramagopal, U.A., Almo, S.C.

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: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 57.51 kDa 
• Atom Count: 3,760 
• Modeled Residue Count: 484 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ylbA	A, B	261	Escherichia coli	Mutation(s): 0  Gene Names: YLBA, GLXB6, B0515 EC: 3.5.3.26
UniProt
Find proteins for P75713 (Escherichia coli (strain K12)) Explore P75713  Go to UniProtKB:  P75713

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.267 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.026	α = 90
b = 109.026	β = 90
c = 136.612	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-18 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Thirumuruhan, R., Ramagopal, U.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2003-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references