8KGZ | pdb_00008kgz

Crystal structure of single-chain Fv antibody against antigen peptide from SARS-CoV2 S-spike protein

• PDB DOI: https://doi.org/10.2210/pdb8KGZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli K-12, Ovis aries
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-20 Released: 2023-11-08 
• Deposition Author(s): Ma, Q.Q., Zhang, B.L., Cheng, X.Y., Huang, Y.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: 
  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of sheep scFv antibody against an antigen peptide of SARS-CoV2 S-spike protein

Ma, Q.Q., Zheng, B.L., Cheng, X.Y., Huang, Y.Q., Su, Z.D.

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: 86.4 kDa 
• Atom Count: 3,483 
• Modeled Residue Count: 464 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1,scFv	A, B	412	Escherichia coli K-12, Ovis aries This entity is chimeric	Mutation(s): 0  Gene Names: trxA, fipA, tsnC, b3781, JW5856
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.271 (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
DIALS	data scaling
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Ma, Q.Q., Zhang, B.L., Cheng, X.Y., Huang, Y.Q., Su, Z.D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary