1U05 | pdb_00001u05

Crystal structure of protein yfiH from Shigella flexneri, Pfam DUF152

• PDB DOI: https://doi.org/10.2210/pdb1U05/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-12 Released: 2004-08-17 
• Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Conserved Hypothetical Protein

Seetharaman, J., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.95 kDa 
• Atom Count: 3,903 
• Modeled Residue Count: 486 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
orf, conserved hypothetical protein	A, B	243	Shigella flexneri	Mutation(s): 0  EC: 2.4.2.1 (UniProt), 3.5.4.4 (UniProt), 2.4.2.28 (UniProt)
UniProt
Find proteins for A0A384KG77 (Shigella flexneri) Explore A0A384KG77  Go to UniProtKB:  A0A384KG77

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.683	α = 90.25
b = 50.465	β = 96.51
c = 55.265	γ = 90.29

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-08-17
  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: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description