2GK0 | pdb_00002gk0

Structure of Catalytic Elimination Antibody 13G5 from a twinned crystal in space group C2

PDB DOI: https://doi.org/10.2210/pdb2GK0/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2006-03-31 Released: 2007-02-06
Deposition Author(s): Debler, E.W., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.255 (Depositor)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Bifunctional Catalysis of Proton Transfer at an Antibody Active Site.

Muller, R., Debler, E.W., Steinmann, M., Seebeck, F.P., Wilson, I.A., Hilvert, D.

(2007) J Am Chem Soc 129: 460-461

PubMed: 17226987 Search on PubMed
DOI: https://doi.org/10.1021/ja066578b
Primary Citation Related Structures:
2GJZ, 2GK0

Organizational Affiliation

Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg HCI F 339, CH-8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 94.84 kDa
Atom Count: 6,692
Modeled Residue Count: 871
Deposited Residue Count: 876
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalytic elimination antibody 13G5 light chain	A [auth L], C [auth A]	217	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q65ZC0 (Mus musculus) Explore Q65ZC0 Go to UniProtKB: Q65ZC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65ZC0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalytic elimination antibody 13G5 heavy chain	B [auth H], D [auth B]	221	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01867 (Mus musculus) Explore P01867 Go to UniProtKB: P01867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01867
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.255 (Depositor)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.236 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.875	α = 90
b = 84.619	β = 90.03
c = 150.074	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
DENZO	data reduction
AMoRE	phasing
SHELXL-97	refinement
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-30
Changes: 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.