4J4K | pdb_00004j4k

Crystal structure of glucose isomerase

PDB DOI: https://doi.org/10.2210/pdb4J4K/pdb

Classification: HYDROLASE
Organism(s): Streptomyces pseudogriseolus
Mutation(s): No

Deposited: 2013-02-07 Released: 2014-04-30
Deposition Author(s): Kim, M.K., An, Y.J., Lee, S., Jeong, C.S., Cha, S.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.163 (Depositor), 0.173 (DCC)
R-Value Work:
0.141 (Depositor), 0.153 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4J4K

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of glucose isomerase

Kim, M.K., An, Y.J., Lee, S., Jeong, C.S., Cha, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 43.9 kDa
Atom Count: 3,518
Modeled Residue Count: 385
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces pseudogriseolus	Mutation(s): 0 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
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.163 (Depositor), 0.173 (DCC)
R-Value Work: 0.141 (Depositor), 0.153 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.927	α = 90
b = 98.867	β = 90
c = 102.638	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.