1Y23

Crystal structure of a member of HIT family of proteins from bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1Y23/pdb

• Classification: CELL CYCLE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-11-19 Released: 2004-12-07 
• Deposition Author(s): Rajashankar, K.R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Crystal structure of a member of HIT family of proteins from bacillus subtilis

Rajashankar, K.R., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.96 kDa 
• Atom Count: 5,854 
• Modelled Residue Count: 698 
• Deposited Residue Count: 725 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad protein	A, B, C, D, E	145	Bacillus subtilis	Mutation(s): 0  Gene Names: yhaE, HIT
UniProt
Find proteins for O07513 (Bacillus subtilis (strain 168)) Explore O07513  Go to UniProtKB:  O07513

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth B], I [auth C], J [auth D], K [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.444	α = 90
b = 86.444	β = 90
c = 180.046	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-07 
Deposition Author(s): Rajashankar, K.R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-12-07
  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: 2018-10-03
  Changes: Data collection, Derived calculations
• Version 1.4: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references
• Version 1.6: 2024-04-03
  Changes: Refinement description