5AVN | pdb_00005avn

The 1.03 angstrom structure (P212121) of glucose isomerase crystallized in high-strength agarose hydrogel

PDB DOI: https://doi.org/10.2210/pdb5AVN/pdb

Classification: ISOMERASE
Organism(s): Streptomyces pseudogriseolus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-23 Released: 2015-07-08
Deposition Author(s): Sugiyama, S., Shimizu, N., Maruyama, N., Sazaki, G., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H.
Funding Organization(s): JSPS KAKENHI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.150 (Depositor), 0.150 (DCC)
R-Value Work:
0.127 (Depositor), 0.129 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Growth of protein crystals in hydrogels prevents osmotic shock

Sugiyama, S., Maruyama, M., Sazaki, G., Hirose, M., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Matsumura, H.

(2012) J Am Chem Soc 134: 5786-5789

PubMed: 22435400 Search on PubMed
DOI: https://doi.org/10.1021/ja301584y
Primary Citation Related Structures:
5AVD, 5AVG, 5AVH, 5AVN

PubMed Abstract:
High-throughput protein X-ray crystallography offers a significant opportunity to facilitate drug discovery. The most reliable approach is to determine the three-dimensional structure of the protein-ligand complex by soaking the ligand in apo crystals. However, protein apo crystals produced by conventional crystallization in a solution are fatally damaged by osmotic shock during soaking. To overcome this difficulty, we present a novel technique for growing protein crystals in a high-concentration hydrogel that is completely gellified and exhibits high strength. This technique allowed us essentially to increase the mechanical stability of the crystals, preventing serious damage to the crystals caused by osmotic shock. Thus, this method may accelerate structure-based drug discoveries.

Organizational Affiliation

Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. sugiyama@chem.eng.osaka-u.ac.jp

Macromolecule Content

Total Structure Weight: 86.88 kDa
Atom Count: 7,812
Modeled Residue Count: 774
Deposited Residue Count: 774
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A, B	387	Streptomyces pseudogriseolus	Mutation(s): 0 Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300 Go to UniProtKB: P24300
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.150 (Depositor), 0.150 (DCC)
R-Value Work: 0.127 (Depositor), 0.129 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.082	α = 90
b = 98.285	β = 90
c = 85.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	23860028
JSPS KAKENHI	Japan	25650051
JSPS KAKENHI	Japan	25286051

Revision History (Full details and data files)

Version 1.0: 2015-07-08
Type: Initial release
Version 1.1: 2020-02-26
Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description