3KCH

Baranase crosslinked by glutaraldehyde

PDB DOI: https://doi.org/10.2210/pdb3KCH/pdb

Classification: HYDROLASE
Organism(s): Bacillus amyloliquefaciens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-21 Released: 2010-03-09
Deposition Author(s): Prange, T., Salem, M., Mauguen, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.185
R-Value Work: 0.145
R-Value Observed: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Revisiting glutaraldehyde cross-linking: the case of the Arg-Lys intermolecular doublet

Salem, M., Mauguen, Y., Prange, T.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 225-228

PubMed: 20208148 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309109054037
Primary Citation of Related Structures:
3KCH

PubMed Abstract:
In addition to the common use of glutaraldehyde to nonspecifically cross-link protein crystals through lysine residues disposed on the surface of the protein, the use of gentle vapour diffusion of glutaraldehyde offers a convenient way to limit polymerization and to allow slow diffusion throughout the crystal. In the case of trimeric barnase crystals, a specific cross-link was observed between an lysine side chain and an arginine side chain that were spatially disposed at the ideal distance on the protein surface in the three monomers. Here, the direct observation of a specific Lys-Arg cross-link site is reported and a mechanism is proposed for the reaction.

Organizational Affiliation

Laboratoire de Cristallographie et RMN Biologiques (UMR 8015 CNRS), Faculté de Pharmacie, Université Descartes, 4 Avenue de l'Observatoire, 75006 Paris, France. michele.salem@parisdescartes.fr

Macromolecule Content

Total Structure Weight: 37.5 kDa
Atom Count: 2,863
Modelled Residue Count: 324
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease	A, B, C	110	Bacillus amyloliquefaciens	Mutation(s): 0 EC: 3.1.27
UniProt
Find proteins for P00648 (Bacillus amyloliquefaciens) Explore P00648 Go to UniProtKB: P00648
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00648
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTD Query on PTD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	PENTANEDIAL C₅ H₈ O₂ SXRSQZLOMIGNAQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.185
R-Value Work: 0.145
R-Value Observed: 0.145
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 58.97	β = 90
c = 82.14	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Prange, T.

Salem, M.

Mauguen, Y.

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-05-02
Changes: Database references
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description