2ICU | pdb_00002icu

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb2ICU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-13 Released: 2006-11-07 
• Deposition Author(s): Chen, L., Liu, Z.J., Li, Y., Zhao, M., Rose, J., Ebihara, A., Yokoyama, S., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

Chen, L., Liu, Z.J., Li, Y., Zhao, M., Rose, J., Ebihara, A., Yokoyama, S., Wang, B.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.

Macromolecule Content 

• Total Structure Weight: 51.43 kDa 
• Atom Count: 4,066 
• Modeled Residue Count: 423 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yedK	A, B	229	Escherichia coli K-12	Mutation(s): 4  Gene Names: yedK EC: 3.4 (UniProt), 4 (UniProt)
UniProt
Find proteins for P76318 (Escherichia coli (strain K12)) Explore P76318  Go to UniProtKB:  P76318

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.203 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.687	α = 90
b = 67.366	β = 98.29
c = 75.125	γ = 90

Software Package:

Software Name	Purpose
SCA2STRUCTURE	model building
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SCA2STRUCTURE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-07 
Deposition Author(s): Chen, L., Liu, Z.J., Li, Y., Zhao, M., Rose, J., Ebihara, A., Yokoyama, S., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-11-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-09-13
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.6: 2025-10-22
  Changes: Structure summary