6LFW | pdb_00006lfw

Crystal structure of PCB4scFv(hN56D) in complex with PCB#126

• PDB DOI: https://doi.org/10.2210/pdb6LFW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-03 Released: 2020-12-09 
• Deposition Author(s): Nakamura, T., Yamagata, Y., Morioka, H.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PCB4scFv(hN56D) in complex with PCB#126

Nakamura, T., Morioka, H.

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: 27.58 kDa 
• Atom Count: 2,295 
• Modeled Residue Count: 231 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCB4scFv(hN56D)	A	253	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OMF (Subject of Investigation/LOI)	B [auth A]	1,2,3-tris(chloranyl)-5-(3-chloranyl-4-methoxy-phenyl)benzene C13 H8 Cl4 O ZPWFINDBNFLFDF-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.21	α = 90
b = 92.21	β = 90
c = 51.55	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Nakamura, T., Yamagata, Y., Morioka, H.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary