3FRW | pdb_00003frw

Crystal structure of putative TrpR protein from Ruminococcus obeum

• PDB DOI: https://doi.org/10.2210/pdb3FRW/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Blautia obeum ATCC 29174
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-08 Released: 2009-01-20 
• Deposition Author(s): Osipiuk, J., Keigher, L., Jedrzejczak, R., Babnigg, G., 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: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

X-ray crystal structure of putative TrpR protein from Ruminococcus obeum.

Osipiuk, J., Keigher, L., Jedrzejczak, R., Babnigg, G., 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.15 kDa 
• Atom Count: 6,738 
• Modeled Residue Count: 750 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Trp repressor protein	A, B, C, D, E, F, G, H	107	Blautia obeum ATCC 29174	Mutation(s): 0  Gene Names: RUMOBE_00155
UniProt
Find proteins for A5ZMD8 (Blautia obeum ATCC 29174) Explore A5ZMD8  Go to UniProtKB:  A5ZMD8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	I [auth B], J [auth D], K [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	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:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.601	α = 90
b = 110.991	β = 101.47
c = 77.262	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Osipiuk, J., Keigher, L., Jedrzejczak, R., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-01-22
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary