4KVF | pdb_00004kvf

The crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836

• PDB DOI: https://doi.org/10.2210/pdb4KVF/pdb

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


• Deposited: 2013-05-22 Released: 2013-06-05 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

The crystal structure of a rhamnose ABC transporter, periplasmic rhamnose-binding protein from Kribbella flavida DSM 17836

Tan, K., Hatzos-Skintges, C., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.87 kDa 
• Atom Count: 2,485 
• Modeled Residue Count: 314 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhamnose ABC transporter, periplasmic rhamnose-binding protein	A	342	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_0259
UniProt
Find proteins for D2PT67 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PT67  Go to UniProtKB:  D2PT67

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.72 Å
• R-Value Free:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.274	α = 90
b = 78.451	β = 90
c = 49.705	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: 2013-06-05 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary