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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.321 (Depositor), 0.318 (DCC)
R-Value Work:
0.269 (Depositor), 0.281 (DCC)
R-Value Observed:
0.271 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AA25
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.321 (Depositor), 0.318 (DCC)
R-Value Work: 0.269 (Depositor), 0.281 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.