5ZZU | pdb_00005zzu

Crystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli- complex with Zn

PDB DOI: https://doi.org/10.2210/pdb5ZZU/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-04 Released: 2019-06-05
Deposition Author(s): Zhao, Y.Q., Cheng, W., Gu, Y.J.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.197 (Depositor), 0.198 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli

Zhao, Y.Q., Lai, Y.J., Zhou, D., Dou, C., Gu, Y.J., Nie, C.L., Wei, Y.Q., Cheng, W.

To be published.

Macromolecule Content

Total Structure Weight: 138.21 kDa
Atom Count: 9,344
Modeled Residue Count: 1,063
Deposited Residue Count: 1,182
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoethanolamine transferase EptC	A, B, C	394	Escherichia coli K-12	Mutation(s): 0 Gene Names: eptC, cptA, yijP, b3955, JW3927 EC: 2.7
UniProt
Find proteins for P0CB39 (Escherichia coli (strain K12)) Explore P0CB39 Go to UniProtKB: P0CB39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CB39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.197 (Depositor), 0.198 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.06	α = 90
b = 85.06	β = 90
c = 121.34	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXS	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570842

Revision History (Full details and data files)

Version 1.0: 2019-06-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.