6UZI | pdb_00006uzi

Crystal structure of Dihydrolipoyl dehydrogenase from Elizabethkingia anophelis NUHP1

PDB DOI: https://doi.org/10.2210/pdb6UZI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-11-15 Released: 2020-01-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.230 (Depositor), 0.209 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

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 Dihydrolipoyl dehydrogenase from Elizabethkingia anophelis NUHP1

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

To be published.

Macromolecule Content

Total Structure Weight: 208.43 kDa
Atom Count: 14,122
Modeled Residue Count: 1,870
Deposited Residue Count: 1,900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B, C, D	475	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: BD94_2540 EC: 1.8.1.4
UniProt
Find proteins for A0A077ELH4 (Elizabethkingia anophelis NUHP1) Explore A0A077ELH4 Go to UniProtKB: A0A077ELH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A077ELH4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B], P [auth C], U [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain U [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain Q [auth C] SDF format, chain L [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth A] mmCIF format, chain F [auth A]	F [auth A], L [auth A], Q [auth C], T [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth A] Focus chain Q [auth C] Focus chain T [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain O [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] MOL2 format, chain S [auth C] MOL2 format, chain O [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] mmCIF format, chain S [auth C] mmCIF format, chain O [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]	H [auth A] I [auth A] J [auth A] K [auth A] O [auth B] H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.230 (Depositor), 0.209 (DCC)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.171 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.06	α = 90
b = 106.8	β = 90
c = 255.7	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary