2DBN | pdb_00002dbn

Crystal Structure of a Hypothetical Protein JW0805 at High pH from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2DBN/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-15 Released: 2006-06-15 
• Deposition Author(s): Ihsanawati, Murayama, K., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of a Hypothetical Protein JW0805 at High pH from Escherichia coli

Ihsanawati, Murayama, K., Bessho, Y., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.21 kDa 
• Atom Count: 3,896 
• Modeled Residue Count: 403 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybiU	A	461	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P75791 (Escherichia coli (strain K12)) Explore P75791  Go to UniProtKB:  P75791

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.688	α = 90
b = 69.688	β = 90
c = 174.649	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-15 
Deposition Author(s): Ihsanawati, Murayama, K., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-06-15
  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: 2024-03-13
  Changes: Data collection, Database references, Derived calculations