2APW | pdb_00002apw

Crystal Structure of the G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V variant of the murine T cell receptor V beta 8.2 domain

PDB DOI: https://doi.org/10.2210/pdb2APW/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-08-16 Released: 2006-03-21
Deposition Author(s): Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.617 (DCC)
R-Value Work:
0.197 (Depositor), 0.586 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2APW

This is version 1.5 of the entry. See complete history.

Literature

Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.

Cho, S., Swaminathan, C.P., Yang, J., Kerzic, M.C., Guan, R., Kieke, M.C., Kranz, D.M., Mariuzza, R.A., Sundberg, E.J.

(2005) Structure 13: 1775-1787

PubMed: 16338399 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2005.11.001
Primary Citation Related Structures:
2APB, 2APF, 2APT, 2APV, 2APW, 2APX, 2AQ1, 2AQ2, 2AQ3

Macromolecule Content

Total Structure Weight: 12.28 kDa
Atom Count: 948
Modeled Residue Count: 109
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain V	A	112	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P04213 (Mus musculus) Explore P04213 Go to UniProtKB: P04213
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04213
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA 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]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-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: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.617 (DCC)
R-Value Work: 0.197 (Depositor), 0.586 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.521	α = 90
b = 74.552	β = 90
c = 113.045	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-03-21

Deposition Author(s):

Swaminathan, C.P.

Revision History (Full details and data files)

Version 1.0: 2006-03-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2015-04-29
Changes: Non-polymer description
Version 1.4: 2018-04-04
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.