2R8R | pdb_00002r8r

Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000

• PDB DOI: https://doi.org/10.2210/pdb2R8R/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-09-11 Released: 2007-09-25 
• Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000.

Nocek, B., Mulligan, R., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.53 kDa 
• Atom Count: 3,699 
• Modeled Residue Count: 416 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A, B	228	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0  Gene Names: kdpD, PSPTO_2245 EC: 2.7.13.3
UniProt
Find proteins for Q883V3 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q883V3  Go to UniProtKB:  Q883V3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.859	α = 90
b = 56.859	β = 90
c = 372.783	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL2Map	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary