5IXP | pdb_00005ixp

Crystal structure of Extracellular solute-binding protein family 1

• PDB DOI: https://doi.org/10.2210/pdb5IXP/pdb

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


• Deposited: 2016-03-23 Released: 2016-03-30 
• Deposition Author(s): Chang, C., Cuff, M., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Crystal structure of Extracellular solute-binding protein family 1

Chang, C., Cuff, M., Chhor, G., 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: 43.97 kDa 
• Atom Count: 3,557 
• Modeled Residue Count: 393 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 1	A	393	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_2403
UniProt
Find proteins for D2PV11 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PV11  Go to UniProtKB:  D2PV11

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A], C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 1.73 Å
• R-Value Free:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.967	α = 90
b = 115.184	β = 131.17
c = 59.976	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Chang, C., Cuff, M., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary