2PKH | pdb_00002pkh

Structural Genomics, the crystal structure of the C-terminal domain of histidine utilization repressor from Pseudomonas syringae pv. tomato str. DC3000

• PDB DOI: https://doi.org/10.2210/pdb2PKH/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pseudomonas syringae pv. tomato str. DC3000
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-04-17 Released: 2007-05-15 
• Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.277 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

The crystal structure of the C-terminal domain of histidine utilization repressor from Pseudomonas syringae pv. tomato str. DC3000.

Tan, K., Zhou, M., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 136.74 kDa 
• Atom Count: 10,115 
• Modeled Residue Count: 1,132 
• Deposited Residue Count: 1,184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine utilization repressor	A, B, C, D, E, F, G, H	148	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 2  Gene Names: hutC, PSPTO5172
UniProt
Find proteins for Q87UX0 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q87UX0  Go to UniProtKB:  Q87UX0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth F], FA [auth F], GA [auth F], HA [auth G], I [auth A], IA [auth G], J [auth A], JA [auth H], K [auth A], KA [auth H], L [auth A], LA [auth H], M [auth A], MA [auth H], N [auth B], NA [auth H], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], U [auth C], V [auth C], W [auth D], X [auth D], Y [auth D], Z [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.277 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.845	α = 90
b = 100.955	β = 90
c = 130.187	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary