1Z67 | pdb_00001z67

Structure of Homeodomain-like Protein of Unknown Function S4005 from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb1Z67/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-03-21 Released: 2005-05-03 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Dementieva, I., Clancy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.208 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif.

Osipiuk, J., Maltseva, N., Dementieva, I., Clancy, S., Collart, F., Joachimiak, A.

(2006) Proteins 65: 509-513

• PubMed: 16927377 
• DOI: https://doi.org/10.1002/prot.21054
• Primary Citation Related Structures: 
  1Z67

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Organizational Affiliation: 
• Biosciences Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.26 kDa 
• Atom Count: 1,172 
• Modeled Residue Count: 127 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein S4005	A	135	Shigella flexneri 2a str. 2457T	Mutation(s): 2  Gene Names: yidB
UniProt
Find proteins for A0A384K8I9 (Shigella flexneri) Explore A0A384K8I9  Go to UniProtKB:  A0A384K8I9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.208 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.476	α = 90
b = 40.479	β = 93.78
c = 48.333	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Osipiuk, J., Maltseva, N., Dementieva, I., Clancy, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary