6PXA | pdb_00006pxa

The crystal structure of chloramphenicol acetyltransferase-like protein from Vibrio fischeri ES114 in complex with taurocholic acid

PDB DOI: https://doi.org/10.2210/pdb6PXA/pdb

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

Deposited: 2019-07-25 Released: 2019-09-25
Deposition Author(s): Tan, K., Maltseva, N., Jedrzejczak, R., Kuhn, M., 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: 1.82 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (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

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc : e0020025-e0020025

PubMed: 40391899 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/mra.00200-25
Primary Citation Related Structures:
5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5UMG, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V0I, 5V36, 5VDN, 5VFB, 5VH6, 5VT3, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NBK, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, ... Search all related entries

PubMed Abstract:
Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

Organizational Affiliation

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 305.23 kDa
Atom Count: 22,056
Modeled Residue Count: 2,622
Deposited Residue Count: 2,652
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloramphenicol acetyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5DZD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TCH (Subject of Investigation/LOI) Query on TCH Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain SA [auth J] SDF format, chain R [auth B] SDF format, chain PA [auth I] SDF format, chain NA [auth H] SDF format, chain M [auth A] SDF format, chain HA [auth G] SDF format, chain GB [auth L] SDF format, chain DA [auth F] SDF format, chain BB [auth K] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain NA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain GB [auth L] MOL2 format, chain DA [auth F] MOL2 format, chain BB [auth K] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain NA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain GB [auth L] mmCIF format, chain DA [auth F] mmCIF format, chain BB [auth K] mmCIF format, chain AA [auth E]	AA [auth E] BB [auth K] DA [auth F] GB [auth L] HA [auth G] AA [auth E], BB [auth K], DA [auth F], GB [auth L], HA [auth G], M [auth A], NA [auth H], PA [auth I], R [auth B], SA [auth J], U [auth C], X [auth D]	TAUROCHOLIC ACID C₂₆ H₄₅ N O₇ S WBWWGRHZICKQGZ-HZAMXZRMSA-N		Interactions Focus chain AA [auth E] Focus chain BB [auth K] Focus chain DA [auth F] Focus chain GB [auth L] Focus chain HA [auth G] Focus chain M [auth A] Focus chain NA [auth H] Focus chain PA [auth I] Focus chain R [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BB [auth K] Focus chain DA [auth F] Focus chain GB [auth L] Focus chain HA [auth G] Focus chain M [auth A] Focus chain NA [auth H] Focus chain PA [auth I] Focus chain R [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain WA [auth J] SDF format, chain VA [auth J] SDF format, chain O [auth A] SDF format, chain LA [auth G] MOL2 format, chain WA [auth J] MOL2 format, chain VA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth G] mmCIF format, chain WA [auth J] mmCIF format, chain VA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth G]	LA [auth G], O [auth A], VA [auth J], WA [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain LA [auth G] Focus chain O [auth A] Focus chain VA [auth J] Focus chain WA [auth J] Interactions & Density Focus chain LA [auth G] Focus chain O [auth A] Focus chain VA [auth J] Focus chain WA [auth J]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain RA [auth I] SDF format, chain OA [auth H] SDF format, chain GA [auth F] SDF format, chain CA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain OA [auth H] MOL2 format, chain GA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain OA [auth H] mmCIF format, chain GA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] GA [auth F] OA [auth H] RA [auth I] T [auth B] CA [auth E], GA [auth F], OA [auth H], RA [auth I], T [auth B], W [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain OA [auth H] Focus chain RA [auth I] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain MA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain MA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain MA [auth G]	MA [auth G], P [auth A], Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain MA [auth G] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain MA [auth G] Focus chain P [auth A] Focus chain Q [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain ZA [auth J] SDF format, chain YA [auth J] SDF format, chain XA [auth J] SDF format, chain FB [auth K] SDF format, chain EB [auth K] SDF format, chain DB [auth K] SDF format, chain AB [auth J] MOL2 format, chain ZA [auth J] MOL2 format, chain YA [auth J] MOL2 format, chain XA [auth J] MOL2 format, chain FB [auth K] MOL2 format, chain EB [auth K] MOL2 format, chain DB [auth K] MOL2 format, chain AB [auth J] mmCIF format, chain ZA [auth J] mmCIF format, chain YA [auth J] mmCIF format, chain XA [auth J] mmCIF format, chain FB [auth K] mmCIF format, chain EB [auth K] mmCIF format, chain DB [auth K] mmCIF format, chain AB [auth J]	AB [auth J] DB [auth K] EB [auth K] FB [auth K] XA [auth J] AB [auth J], DB [auth K], EB [auth K], FB [auth K], XA [auth J], YA [auth J], ZA [auth J]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FB [auth K] Focus chain XA [auth J] Focus chain YA [auth J] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain DB [auth K] Focus chain EB [auth K] Focus chain FB [auth K] Focus chain XA [auth J] Focus chain YA [auth J] Focus chain ZA [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain UA [auth J] SDF format, chain TA [auth J] SDF format, chain S [auth B] SDF format, chain QA [auth I] SDF format, chain N [auth A] SDF format, chain KA [auth G] SDF format, chain JA [auth G] SDF format, chain IB [auth L] SDF format, chain IA [auth G] SDF format, chain HB [auth L] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain CB [auth K] SDF format, chain BA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth J] MOL2 format, chain TA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain IB [auth L] MOL2 format, chain IA [auth G] MOL2 format, chain HB [auth L] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain CB [auth K] MOL2 format, chain BA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth J] mmCIF format, chain TA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain IB [auth L] mmCIF format, chain IA [auth G] mmCIF format, chain HB [auth L] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain CB [auth K] mmCIF format, chain BA [auth E]	BA [auth E] CB [auth K] EA [auth F] FA [auth F] HB [auth L] BA [auth E], CB [auth K], EA [auth F], FA [auth F], HB [auth L], IA [auth G], IB [auth L], JA [auth G], KA [auth G], N [auth A], QA [auth I], S [auth B], TA [auth J], UA [auth J], V [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HB [auth L] Focus chain IA [auth G] Focus chain IB [auth L] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth A] Focus chain QA [auth I] Focus chain S [auth B] Focus chain TA [auth J] Focus chain UA [auth J] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HB [auth L] Focus chain IA [auth G] Focus chain IB [auth L] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth A] Focus chain QA [auth I] Focus chain S [auth B] Focus chain TA [auth J] Focus chain UA [auth J] Focus chain V [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.519	α = 89.399
b = 121.363	β = 89.911
c = 146.17	γ = 87.602

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-25

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	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2019-09-25
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
Version 1.3: 2025-06-18
Changes: Database references, Structure summary