7DMM | pdb_00007dmm

Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants

PDB DOI: https://doi.org/10.2210/pdb7DMM/pdb

Classification: ISOMERASE
Organism(s): Streptomyces pseudogriseolus
Mutation(s): Yes

Deposited: 2020-12-04 Released: 2021-12-08
Deposition Author(s): Suzuki, Y., Maita, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free:
0.166 (Depositor), 0.174 (DCC)
R-Value Work:
0.157 (Depositor), 0.167 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Extraordinarily fast growth of high-quality glucose isomerase crystals simply by concentration in a precipitant-free solution with a cryoprotectant

Suzuki, Y., Ikemitsu, N., Maita, N.

To be published.

Macromolecule Content

Total Structure Weight: 43.4 kDa
Atom Count: 3,460
Modeled Residue Count: 386
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	386	Streptomyces pseudogriseolus	Mutation(s): 1 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
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free: 0.166 (Depositor), 0.174 (DCC)
R-Value Work: 0.157 (Depositor), 0.167 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.61	α = 90
b = 98.46	β = 90
c = 102.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K04960

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.