3MAJ | pdb_00003maj

Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris CGA009

• PDB DOI: https://doi.org/10.2210/pdb3MAJ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-23 Released: 2010-05-12 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of putative DNA processing protein DprA from Rhodopseudomonas palustris

Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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: 40.52 kDa 
• Atom Count: 2,762 
• Modeled Residue Count: 353 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA processing chain A	A	382	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: DprA, RPA3120
UniProt
Find proteins for Q6N563 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N563  Go to UniProtKB:  Q6N563

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.215	α = 90
b = 44.33	β = 90
c = 75.81	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary