3DCA | pdb_00003dca

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

• PDB DOI: https://doi.org/10.2210/pdb3DCA/pdb

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


• Deposited: 2008-06-03 Released: 2008-08-05 
• Deposition Author(s): Sledz, P., Wang, S., Chruszcz, M., Yim, V., Kudritska, M., Evdokimova, E., Turk, D., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.273 (Depositor), 0.274 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Literature

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

Sledz, P., Wang, S., Chruszcz, M., Yim, V., Kudritska, M., Evdokimova, E., Turk, D., Savchenko, A., Edwards, A., Minor, W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.66 kDa 
• Atom Count: 3,894 
• Modeled Residue Count: 520 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	A, B, C, D	142	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90  Go to UniProtKB:  Q6NC90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], H [auth C], I [auth D], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 3.35 Å
• R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.273 (Depositor), 0.274 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.495	α = 90
b = 193.495	β = 90
c = 118.848	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
MAIN	model building
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
MAIN	phasing
MAIN	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Sledz, P., Wang, S., Chruszcz, M., Yim, V., Kudritska, M., Evdokimova, E., Turk, D., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary