9JPV | pdb_00009jpv

A Fab Fragment of IgG

PDB DOI: https://doi.org/10.2210/pdb9JPV/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-09-26 Released: 2025-10-01
Deposition Author(s): Makabe, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.223 (Depositor)

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

This is version 1.0 of the entry. See complete history.

Literature

Structure of Fab Fragment of IgG

Makabe, K., Nakanishi, T., Tachibana, T.

To be published.

Macromolecule Content

Total Structure Weight: 95.27 kDa
Atom Count: 6,951
Modeled Residue Count: 854
Deposited Residue Count: 880
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-VHCH1-1	A, C	222	Rattus norvegicus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-CL-1	B, D	218	Rattus norvegicus	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: 1.94 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.222 (Depositor), 0.223 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.991	α = 90
b = 100.991	β = 90
c = 213.473	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
Coot	model building
XDS	data reduction
AMoRE	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release

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.