4GB5

Crystal structure of Kfla4162 protein from Kribbella flavida

• PDB DOI: https://doi.org/10.2210/pdb4GB5/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-26 Released: 2012-09-26 
• Deposition Author(s): Michalska, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Crystal structure of Kfla4162 protein from Kribbella flavida (CASP Target)

Michalska, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.94 kDa 
• Atom Count: 1,353 
• Modelled Residue Count: 148 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	159	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_4162
UniProt
Find proteins for D2PTS5 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PTS5  Go to UniProtKB:  D2PTS5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A], D [auth A], E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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: 1.55 Å
• R-Value Free:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GB5

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.948	α = 90
b = 57.948	β = 90
c = 81.605	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Michalska, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary