6U9C

The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA

PDB DOI: https://doi.org/10.2210/pdb6U9C/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-07 Released: 2019-09-18
Deposition Author(s): Kim, Y., Maltseva, N., Stam, J., 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: 2.20 Å
R-Value Free: 0.251
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA

Kim, Y., Maltseva, N., Stam, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 74.73 kDa
Atom Count: 5,155
Modelled Residue Count: 624
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloramphenicol acetyltransferase	A, B, C	212	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_A0300
UniProt
Find proteins for Q9KMN1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMN1 Go to UniProtKB: Q9KMN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KMN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C]	F [auth B], H [auth B], K [auth C]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain F [auth B] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain F [auth B] Focus chain H [auth B] Focus chain K [auth C]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain L [auth C]	D [auth A], L [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain L [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C]	I [auth B], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain I [auth B] Focus chain M [auth C]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C]	J [auth B], N [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain J [auth B] Focus chain N [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.251
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.231	α = 90
b = 101.231	β = 90
c = 126.184	γ = 120

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-09-18

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	--

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description

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6U9C

The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA

The 2.2 A Crystal Structure of the Type B Chloramphenicol Acetyltransferase from Vibrio cholerae in the complex with Acetyl CoA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)