3MYF | pdb_00003myf

The Crystal Structure of the HPT domain from the Hpt Sensor Hybrid Histidine Kinase from Shewanella to 1.80A

• PDB DOI: https://doi.org/10.2210/pdb3MYF/pdb

• Classification: TRANSFERASE
• Organism(s): Shewanella sp. W3-18-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-10 Released: 2010-05-26 
• Deposition Author(s): Stein, A.J., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

The Crystal Structure of the HPT domain from the Hpt Sensor Hybrid Histidine Kinase from Shewanella to 1.80A

Stein, A.J., Tesar, C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.82 kDa 
• Atom Count: 3,779 
• Modeled Residue Count: 461 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A, B, C, D	119	Shewanella sp. W3-18-1	Mutation(s): 0  Gene Names: Sputw3181_1245 EC: 2.7.13.3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.271 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.889	α = 90
b = 71.188	β = 90
c = 95.852	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Stein, A.J., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary