6TCT | pdb_00006tct

MakD from the mak operon of Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb6TCT/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-06 Released: 2020-11-18 
• Deposition Author(s): Persson, K., Nagampalli, R., Heidler, T., Wai, S.N.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

MakD from the mak operon of Vibrio cholerae

Persson, K., Nagampalli, R., Heidler, T., Wai, S.N.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.99 kDa 
• Atom Count: 4,155 
• Modeled Residue Count: 500 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MakD	A [auth B], B [auth D], C [auth A], D [auth C]	126	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_A0880
UniProt
Find proteins for Q9KL67 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL67  Go to UniProtKB:  Q9KL67

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.327	α = 90
b = 70.886	β = 90
c = 185.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Persson, K., Nagampalli, R., Heidler, T., Wai, S.N.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-05009
Swedish Research Council	Sweden	2018-02914

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references, Refinement description