8QF3 | pdb_00008qf3

1.25-A structure of anti-Arc nanobody H11

PDB DOI: https://doi.org/10.2210/pdb8QF3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-02 Released: 2024-03-13
Deposition Author(s): Godoy Munoz, J.M., Kursula, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

1.25-A structure of anti-Arc nanobody H11

Godoy Munoz, J.M., Kursula, P.

To be published.

Macromolecule Content

Total Structure Weight: 28.16 kDa
Atom Count: 2,133
Modeled Residue Count: 252
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H11	A [auth E], B [auth A]	128	Vicugna pacos	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: 1.25 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.17	α = 90
b = 57.17	β = 90
c = 145.64	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Godoy Munoz, J.M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release
Version 1.1: 2024-11-13
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.