3UMT | pdb_00003umt

scFv12, Anti-BclA antibody single chain variable fragment

PDB DOI: https://doi.org/10.2210/pdb3UMT/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-14 Released: 2012-11-14
Deposition Author(s): Pokkuluri, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.224 (DCC)
R-Value Work:
0.175 (Depositor)
R-Value Observed:
0.177 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3UMT

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

Literature

Systematic stability engineering of single-chain antibodies

Wilton, R., Londer, Y.Y., Hanson, D.K., Zerbs, S., Dirks, A., Warner, C., Carney, J.P., Pokkuluri, P.R., Stevens, F.J.

To be published.

Macromolecule Content

Total Structure Weight: 27.66 kDa
Atom Count: 1,940
Modeled Residue Count: 227
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv heavy chain and light chain	A	256	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE 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]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.224 (DCC)
R-Value Work: 0.175 (Depositor)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.29	α = 90
b = 65.29	β = 90
c = 96.202	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Pokkuluri, P.R.

Revision History (Full details and data files)

Version 1.0: 2012-11-14
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.