3OKX | pdb_00003okx

Crystal structure of YaeB-like protein from Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb3OKX/pdb

• Classification: structural genomics, unknown function
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-25 Released: 2010-09-08 
• Deposition Author(s): Chang, C., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of YaeB-like protein from Rhodopseudomonas palustris

Chang, C., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., 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: 38.65 kDa 
• Atom Count: 2,796 
• Modeled Residue Count: 305 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YaeB-like protein RPA0152	A, B	169	Rhodopseudomonas palustris CGA009	Mutation(s): 0  Gene Names: RPA0152
UniProt
Find proteins for Q6NDF6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NDF6  Go to UniProtKB:  Q6NDF6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-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: 1.80 Å
• R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.317	α = 90
b = 74.317	β = 90
c = 116.817	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Chang, C., Evdokimova, E., Liu, F., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary