7CVM

Crystal structure of glucose isomerase by fixed-target serial synchrotron crystallography (500 ms)

PDB DOI: https://doi.org/10.2210/pdb7CVM/pdb

Classification: ISOMERASE
Organism(s): Streptomyces rubiginosus
Mutation(s): No

Deposited: 2020-08-26 Released: 2020-09-09
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.248
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

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

Literature

Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Park, S.Y., Choi, H., Eo, C., Cho, Y., Nam, K.H.

(2020) Crystals (Basel) 10

DOI: https://doi.org/10.3390/cryst10090803

Macromolecule Content

Total Structure Weight: 43.33 kDa
Atom Count: 3,382
Modelled Residue Count: 385
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces rubiginosus	Mutation(s): 0 EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300 Go to UniProtKB: P24300
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.248
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.11577/1659492

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.55	α = 90
b = 100.26	β = 90
c = 103.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2022-03-23
Changes: Database references
Version 1.2: 2023-09-06
Changes: Data collection, Database references
Version 1.3: 2023-11-29
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.