7EQ3 | pdb_00007eq3

Apo diabody form of CRH2-directed antibody 9F8

PDB DOI: https://doi.org/10.2210/pdb7EQ3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-04-29 Released: 2022-05-18
Deposition Author(s): Yan, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Tall cytokine receptor signaling fine-tuning through dimer geometric reconstitution

Yan, L.

To be published.

Macromolecule Content

Total Structure Weight: 25.07 kDa
Atom Count: 1,750
Modeled Residue Count: 229
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
9F8 diabody	A	230	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.238 (Depositor), 0.240 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.806	α = 90
b = 106.806	β = 90
c = 50.02	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-05-18
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-09
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.