3ULR | pdb_00003ulr

Lysozyme contamination facilitates crystallization of a hetero-trimericCortactin:Arg:Lysozyme complex

PDB DOI: https://doi.org/10.2210/pdb3ULR/pdb

Classification: HYDROLASE, PROTEIN BINDING
Organism(s): Gallus gallus, Mus musculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-11-11 Released: 2012-01-11
Deposition Author(s): Liu, W., MacGrath, S., Koleske, A.J., Boggon, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.188 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Lysozyme contamination facilitates crystallization of a heterotrimeric cortactin-Arg-lysozyme complex.

Liu, W., Macgrath, S.M., Koleske, A.J., Boggon, T.J.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 154-158

PubMed: 22297987 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309111056132
Primary Citation Related Structures:
3ULR

PubMed Abstract:
Crystallization of contaminating proteins is a frequently encountered problem for macromolecular crystallographers. In this study, an attempt was made to obtain a binary cocrystal structure of the SH3 domain of cortactin and a 17-residue peptide from the Arg nonreceptor tyrosine kinase encompassing a PxxPxxPxxP (PxxP1) motif. However, cocrystals could only be obtained in the presence of trace amounts of a contaminating protein. A structure solution obtained by molecular replacement followed by ARP/wARP automatic model building allowed a 'sequence-by-crystallography' approach to discover that the contaminating protein was lysozyme. This 1.65 Å resolution crystal structure determination of a 1:1:1 heterotrimeric complex of Arg, cortactin and lysozyme thus provides an unusual `caveat emptor' warning of the dangers that underpurified proteins harbor for macromolecular crystallographers.

Organizational Affiliation

Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.

Macromolecule Content

Total Structure Weight: 23.4 kDa
Atom Count: 1,920
Modeled Residue Count: 206
Deposited Residue Count: 211
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Src substrate cortactin	B	65	Mus musculus	Mutation(s): 0 Gene Names: Cttn, Ems1
UniProt & NIH Common Fund Data Resources
Find proteins for Q60598 (Mus musculus) Explore Q60598 Go to UniProtKB: Q60598
IMPC: MGI:99695
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60598
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Abelson tyrosine-protein kinase 2	C	17	Homo sapiens	Mutation(s): 0 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P42684 (Homo sapiens) Explore P42684 Go to UniProtKB: P42684
PHAROS: P42684 GTEx: ENSG00000143322
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42684
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.184 (Depositor), 0.188 (DCC)
R-Value Observed: 0.186 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.658	α = 90
b = 57.838	β = 90
c = 95.513	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-11
Type: Initial release
Version 1.1: 2012-02-15
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary