3C0C | pdb_00003c0c

X-ray Crystal Structure of the Rat Endophilin A2 SH3 Domain

PDB DOI: https://doi.org/10.2210/pdb3C0C/pdb

Classification: ENDOCYTOSIS
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-01-19 Released: 2008-03-18
Deposition Author(s): Loll, P.J., Swain, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.217 (Depositor)
R-Value Work:
0.196 (Depositor), 0.201 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the SH3 domain of rat endophilin A2

Loll, P.J., Swain, E., Chen, Y., Turner, B.T., Zhang, J.

To be published.

Macromolecule Content

Total Structure Weight: 8.3 kDa
Atom Count: 606
Modeled Residue Count: 64
Deposited Residue Count: 73
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endophilin-A2	A	73	Rattus norvegicus	Mutation(s): 0 Gene Names: Sh3gl1, Sh3p8
UniProt
Find proteins for O35964 (Rattus norvegicus) Explore O35964 Go to UniProtKB: O35964
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.217 (Depositor)
R-Value Work: 0.196 (Depositor), 0.201 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.97	α = 90
b = 64.97	β = 90
c = 41.27	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 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.