6K7F

Crystal structure of MBPholo-Tim21 fusion protein with a 17-residue helical linker

• PDB DOI: https://doi.org/10.2210/pdb6K7F/pdb

• Classification: SUGAR BINDING PROTEIN, TRANSLOCASE
• Organism(s): Escherichia coli K-12, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-06-07 Released: 2019-09-18 
• Deposition Author(s): Bala, S., Shimada, A., Kohda, D.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.

Bala, S., Shinya, S., Srivastava, A., Ishikawa, M., Shimada, A., Kobayashi, N., Kojima, C., Tama, F., Miyashita, O., Kohda, D.

(2020) Biochim Biophys Acta Gen Subj 1864: 129418-129418

• PubMed: 31449839 
• DOI: https://doi.org/10.1016/j.bbagen.2019.129418
• Primary Citation of Related Structures:  
  6K7D, 6K7E, 6K7F, 6K8Q


• PubMed Abstract: 
  

  In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules.

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Organizational Affiliation: 

Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.99 kDa 
• Atom Count: 4,264 
• Modelled Residue Count: 499 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Mitochondrial import inner membrane translocase subunit TIM21	A	499	Escherichia coli K-12, Saccharomyces cerevisiae S288C This entity is chimeric	Mutation(s): 1  Gene Names: malE, b4034, JW3994, TIM21, YGR033C
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P53220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53220  Go to UniProtKB:  P53220
UniProt Groups	P0AEX9P53220

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.97	α = 90
b = 69.41	β = 90
c = 171.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Bala, S., Shimada, A., Kohda, D.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP26119002
Japan Society for the Promotion of Science	Japan	JP19H05452

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary