3H5I

Crystal structure of the N-terminal domain of a response regulator/sensory box/GGDEF 3-domain protein from Carboxydothermus hydrogenoformans

• PDB DOI: https://doi.org/10.2210/pdb3H5I/pdb

• Classification: TRANSCRIPTION
• Organism(s): Carboxydothermus hydrogenoformans Z-2901
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-22 Released: 2009-05-05 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Crystal structure of the N-terminal domain of a response regulator/sensory box/GGDEF 3-domain protein from Carboxydothermus hydrogenoformans

Bonanno, J.B., Gilmore, M., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 15.57 kDa 
• Atom Count: 985 
• Modelled Residue Count: 125 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator/sensory box protein/GGDEF domain protein	A	140	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0  Gene Names: CHY_0880
UniProt
Find proteins for Q3ADQ4 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3ADQ4  Go to UniProtKB:  Q3ADQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.238 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.668	α = 90
b = 86.668	β = 90
c = 131.156	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Iizuka, M., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references