3K8R | pdb_00003k8r

Crystal structure of protein of unknown function (YP_427503.1) from Rhodospirillum rubrum ATCC 11170 at 2.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3K8R/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-14 Released: 2009-10-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.235 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of protein of unknown function (YP_427503.1) from Rhodospirillum rubrum ATCC 11170 at 2.75 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 26.96 kDa 
• Atom Count: 1,275 
• Modeled Residue Count: 168 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	124	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: Rru_A2416
UniProt
Find proteins for Q2RRM9 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RRM9  Go to UniProtKB:  Q2RRM9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.75 Å
• R-Value Free:  0.235 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33K8R

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.97	α = 90
b = 111.97	β = 90
c = 45.514	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary