3HTR | pdb_00003htr

Crystal Structure of PRC-barrel Domain Protein from Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb3HTR/pdb

• Classification: structural genomics, unknown function
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-06-12 Released: 2009-07-07 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Kinney, J., Babnigg, G., Harwood, C., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal Structure of PRC-barrel Domain Protein from Rhodopseudomonas palustris

Kim, Y., Tesar, C., Jedrzejczak, R., Kinney, J., Babnigg, G., Harwood, C., Kerfeld, C., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 27.04 kDa 
• Atom Count: 1,554 
• Modeled Residue Count: 188 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized PRC-barrel Domain Protein	A, B	120	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA4758
UniProt
Find proteins for Q6N0K4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N0K4  Go to UniProtKB:  Q6N0K4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	E [auth A], F [auth A], I [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-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: 2.06 Å
• R-Value Free:  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.644	α = 90
b = 63.061	β = 99.39
c = 61.866	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
PHENIX	model building
SOLVE	phasing
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Kinney, J., Babnigg, G., Harwood, C., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary