4OZE | pdb_00004oze

A.aolicus LpxC in complex with native product

PDB DOI: https://doi.org/10.2210/pdb4OZE/pdb

Classification: HYDROLASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-02-15 Released: 2014-08-13
Deposition Author(s): Olivier, N.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.185 (Depositor), 0.180 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (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

Mechanistic insight from the crystal structure of A.aolicus LpxC in the presence of product

Miller, M.D., Gao, N., Ross, P., Olivier, N.B.

To be published.

Macromolecule Content

Total Structure Weight: 66.5 kDa
Atom Count: 5,058
Modeled Residue Count: 533
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	282	Aquifex aeolicus	Mutation(s): 0 Gene Names: lpxC, envA, aq_1772 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for O67648 (Aquifex aeolicus (strain VF5)) Explore O67648 Go to UniProtKB: O67648
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67648
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
24G Query on 24G Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine C₂₉ H₅₁ N₃ O₁₈ P₂ ZFPNNOXCEDQJQS-SSVOXRMNSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] I [auth B] C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.185 (Depositor), 0.180 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.332	α = 90
b = 101.332	β = 90
c = 123.553	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Olivier, N.B.

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2015-02-04
Changes: Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy

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Deposit Data

Help and Resources

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A.aolicus LpxC in complex with native product

Mechanistic insight from the crystal structure of A.aolicus LpxC in the presence of product

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations