6LND | pdb_00006lnd

Crystal structure of transposition protein TniQ

• PDB DOI: https://doi.org/10.2210/pdb6LND/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-28 Released: 2020-02-19 
• Deposition Author(s): Wang, B., Xu, W., Yang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Structural basis of a Tn7-like transposase recruitment and DNA loading to CRISPR-Cas surveillance complex.

Wang, B., Xu, W., Yang, H.

(2020) Cell Res 30: 185-187

• PubMed: 31913359 
• DOI: https://doi.org/10.1038/s41422-020-0274-0
• Primary Citation of Related Structures:  
  6LNB, 6LNC, 6LND

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Organizational Affiliation: 
• State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. [e-mail].

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

Macromolecule Content 

• Total Structure Weight: 46.15 kDa 
• Atom Count: 3,233 
• Modeled Residue Count: 385 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transposition protein TniQ	A [auth K]	396	Vibrio cholerae	Mutation(s): 0
UniProt
Find proteins for A0A6I8WFP2 (Vibrio cholerae) Explore A0A6I8WFP2  Go to UniProtKB:  A0A6I8WFP2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth K], C [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth K]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.277	α = 90
b = 66.277	β = 90
c = 178.584	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Wang, B., Xu, W., Yang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971135)

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary