2O38 | pdb_00002o38

Putative XRE Family Transcriptional Regulator

• PDB DOI: https://doi.org/10.2210/pdb2O38/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-30 Released: 2007-01-02 
• Deposition Author(s): Kim, Y., Joachimiak, A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.271 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

The Crystal Structure of Putative XRE Family Transcriptional Regulator

Kim, Y., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, 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: 26.59 kDa 
• Atom Count: 1,609 
• Modeled Residue Count: 179 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	120	Rhodopseudomonas palustris CGA009	Mutation(s): 3  Gene Names: RPA3824
UniProt
Find proteins for Q6N370 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N370  Go to UniProtKB:  Q6N370

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], D [auth B], E [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: 1.83 Å
• R-Value Free:  0.271 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.994	α = 90
b = 58.276	β = 90
c = 83.459	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Kim, Y., Joachimiak, A., Evdokimova, E., Kagan, O., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary