6LEW | pdb_00006lew

RVD HA specifically contacts 5mC through van der Waals interactions

• PDB DOI: https://doi.org/10.2210/pdb6LEW/pdb
• NAKB: 6LEW

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xanthomonas campestris pv. armoraciae, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-27 Released: 2020-12-02 
• Deposition Author(s): Liu, L., Yi, C.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

RVD HA specifically contacts 5mC through van der Waals interactions

Liu, L., Yi, C.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 124.61 kDa 
• Atom Count: 7,965 
• Modeled Residue Count: 968 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TAL effector	A, D [auth B]	499	Xanthomonas campestris pv. armoraciae	Mutation(s): 0
UniProt
Find proteins for Q3ZD72 (Xanthomonas campestris pv. armoraciae) Explore Q3ZD72  Go to UniProtKB:  Q3ZD72

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')	B [auth I], E [auth C]	17	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')	C [auth J], F [auth D]	17	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.786	α = 90
b = 88.022	β = 104.77
c = 89.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Liu, L., Yi, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21825701
National Natural Science Foundation of China	China	91740112

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description