4OAD | pdb_00004oad

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with chloramphenicol

PDB DOI: https://doi.org/10.2210/pdb4OAD/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-04 Released: 2014-01-29
Deposition Author(s): Majorek, K.A., Niedzialkowska, E., Chruszcz, M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.179 (Depositor), 0.180 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with chloramphenicol

Majorek, K.A., Niedzialkowska, E., Chruszcz, M., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 19.53 kDa
Atom Count: 1,644
Modeled Residue Count: 160
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GNAT superfamily acetyltransferase PA4794	A	162	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA4794
UniProt
Find proteins for Q9HV14 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HV14 Go to UniProtKB: Q9HV14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HV14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLM Query on CLM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORAMPHENICOL C₁₁ H₁₂ Cl₂ N₂ O₅ WIIZWVCIJKGZOK-RKDXNWHRSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.179 (Depositor), 0.180 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.754	α = 90
b = 76.072	β = 90
c = 39.483	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Refinement description