7KN1 | pdb_00007kn1

Crystal structure of UDP-glucose-4-epimerase (galE) from Stenotrophomonas maltophila with bound NAD and formylated UDP-arabinopyranose

PDB DOI: https://doi.org/10.2210/pdb7KN1/pdb

Classification: ISOMERASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-03 Released: 2020-11-11
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.177 (Depositor), 0.186 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of UDP-glucose-4-epimerase (galE) from Stenotrophomonas maltophila with bound NAD and formylated UDP-arabinopyranose

Bolejack, M.J., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 80.11 kDa
Atom Count: 6,382
Modeled Residue Count: 672
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A, B	354	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: galE, Smlt3413 EC: 5.1.3.2
UniProt
Find proteins for B2FNY6 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FNY6 Go to UniProtKB: B2FNY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2FNY6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], M [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
WQD Query on WQD Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain L [auth A]	L [auth A], T [auth B]	UDP-4-deoxy-4-formamido-beta-L-arabinopyranose C₁₅ H₂₃ N₃ O₁₆ P₂ QGYFHZBDXXNYAX-RTXATJJPSA-N		Interactions Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.177 (Depositor), 0.186 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.27	α = 90
b = 79.42	β = 90
c = 153.85	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2021-07-21
Changes: Other, Structure summary
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description