5UX9

The crystal structure of chloramphenicol acetyltransferase from Vibrio fischeri ES114

PDB DOI: https://doi.org/10.2210/pdb5UX9/pdb

Classification: TRANSFERASE
Organism(s): Aliivibrio fischeri ES114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-22 Released: 2017-03-08
Deposition Author(s): Tan, K., Zhou, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.240
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of chloramphenicol acetyltransferase from Vibrio fischeri ES114

Tan, K., Zhou, M., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 101.99 kDa
Atom Count: 6,910
Modelled Residue Count: 862
Deposited Residue Count: 884
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloramphenicol acetyltransferase	A, B, C, D	221	Aliivibrio fischeri ES114	Mutation(s): 0 Gene Names: VF_A0790 EC: 2.3.1.28
UniProt
Find proteins for Q5DZD6 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DZD6 Go to UniProtKB: Q5DZD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5DZD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	E [auth A] J [auth B] P [auth C] Q [auth C] V [auth D] E [auth A], J [auth B], P [auth C], Q [auth C], V [auth D], W [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	G [auth A] H [auth A] L [auth B] S [auth C] T [auth C] G [auth A], H [auth A], L [auth B], S [auth C], T [auth C], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain AA [auth D]	AA [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Interactions & Density Focus chain AA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	I [auth A] M [auth B] N [auth B] O [auth B] U [auth C] I [auth A], M [auth B], N [auth B], O [auth B], U [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	F [auth A], K [auth B], R [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain X [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.240
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.426	α = 90
b = 147.426	β = 90
c = 101.211	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary