8JUH | pdb_00008juh

Crystal structure of ScFv against the receptor binding domine of SARS-CoV-2 S-spike protein

• PDB DOI: https://doi.org/10.2210/pdb8JUH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Ovis aries
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-26 Released: 2023-08-23 
• Deposition Author(s): Ma, Q.Q., Su, Z.D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.310 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of ScFv against the receptor binding domine of SARS-CoV-2 S-spike protein

Ma, Q.Q., Su, Z.D., Song, S.K., Zhang, B.L., Cheng, X.Y.

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 (software)

Macromolecule Content 

• Total Structure Weight: 50.06 kDa 
• Atom Count: 3,349 
• Modeled Residue Count: 454 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single chain fab antibody	A, B [auth C]	245	Ovis aries	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.310 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.21	α = 90
b = 77.753	β = 112.25
c = 61.346	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Ma, Q.Q., Su, Z.D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-08-23
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary