3DM8 | pdb_00003dm8

Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb3DM8/pdb

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


• Deposited: 2008-06-30 Released: 2008-08-05 
• Deposition Author(s): Cymborowski, M., Chruszcz, M., Skarina, T., Kagan, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris

Cymborowski, M., 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)

Macromolecule Content 

• Total Structure Weight: 16.94 kDa 
• Atom Count: 1,280 
• Modeled Residue Count: 135 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein RPA4348	A	143	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA4348
UniProt
Find proteins for Q6N1Q6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N1Q6  Go to UniProtKB:  Q6N1Q6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CE9	B [auth A]	DODECYL NONA ETHYLENE GLYCOL ETHER C30 H62 O10 ONJQDTZCDSESIW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.216 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.593	α = 90
b = 84.071	β = 90
c = 97.211	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Cymborowski, M., Chruszcz, M., Skarina, T., Kagan, O., Savchenko, A., Edwards, A.M., 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: Advisory, Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection