6X7Q | pdb_00006x7q

Chloramphenicol acetyltransferase type III in complex with chloramphenicol and acetyl-oxa(dethia)-CoA

PDB DOI: https://doi.org/10.2210/pdb6X7Q/pdb

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

Deposited: 2020-05-30 Released: 2021-06-02
Deposition Author(s): Benjamin, A.B., Stunkard, L.M., Ling, J., Nice, J.N., Lohman, J.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.201 (Depositor), 0.211 (DCC)
R-Value Work:
0.159 (Depositor), 0.172 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-keto-acylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(de-thia)CoA

Benjamin, A.B., Stunkard, L.M., Ling, J., Nice, J.N., Lohman, J.R.

(2023) Acta Crystallogr F Struct Biol Commun : 61-69

DOI: https://doi.org/10.1107/S2053230X23001206

Macromolecule Content

Total Structure Weight: 79.06 kDa
Atom Count: 6,530
Modeled Residue Count: 638
Deposited Residue Count: 645
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloramphenicol acetyltransferase 3	A, B, C	215	Escherichia coli	Mutation(s): 0 Gene Names: cat3 EC: 2.3.1.28
UniProt
Find proteins for P00484 (Escherichia coli) Explore P00484 Go to UniProtKB: P00484
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00484
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UTA (Subject of Investigation/LOI) Query on UTA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], L [auth C]	acetyl-oxa(dethia)-CoA C₂₃ H₃₈ N₇ O₁₈ P₃ YTFJZNGIRMRBLL-ZSJPKINUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C]
CLM Query on CLM Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], K [auth C]	CHLORAMPHENICOL C₁₁ H₁₂ Cl₂ N₂ O₅ WIIZWVCIJKGZOK-RKDXNWHRSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain E [auth A]	E [auth A], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.201 (Depositor), 0.211 (DCC)
R-Value Work: 0.159 (Depositor), 0.172 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.918	α = 90
b = 106.918	β = 90
c = 126.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM140290

Revision History (Full details and data files)

Version 1.0: 2021-06-02
Type: Initial release
Version 2.0: 2022-07-20
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
Version 2.1: 2023-03-08
Changes: Database references
Version 2.2: 2023-10-25
Changes: Data collection, Refinement description