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

Experimental Data Snapshot

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

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

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

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.

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single chain fab antibody	A, B [auth C]	245	Ovis aries	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

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Entry History & Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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.