4NOC | pdb_00004noc

The crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.

• PDB DOI: https://doi.org/10.2210/pdb4NOC/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-19 Released: 2013-11-27 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

The crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.

Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.63 kDa 
• Atom Count: 4,347 
• Modeled Residue Count: 576 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative signal transduction protein with CBS domains	A, B, C, D	151	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_0464
UniProt
Find proteins for D2PVT0 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PVT0  Go to UniProtKB:  D2PVT0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth D], P [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.434	α = 90
b = 99.434	β = 90
c = 260.582	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary