6PXA

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
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

Tan, K., Maltseva, N., Jedrzejczak, R., Kuhn, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 305.23 kDa
Atom Count: 22,056
Modelled Residue Count: 2,622
Deposited Residue Count: 2,652
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, 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AA [auth E] SDF format, chain BB [auth K] SDF format, chain DA [auth F] SDF format, chain GB [auth L] SDF format, chain HA [auth G] SDF format, chain M [auth A] SDF format, chain NA [auth H] SDF format, chain PA [auth I] SDF format, chain R [auth B] SDF format, chain SA [auth J] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BB [auth K] MOL2 format, chain DA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain PA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D]	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 LA [auth G] SDF format, chain O [auth A] SDF format, chain VA [auth J] SDF format, chain WA [auth J] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain VA [auth J] MOL2 format, chain WA [auth J]	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 CA [auth E] SDF format, chain GA [auth F] SDF format, chain OA [auth H] SDF format, chain RA [auth I] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain OA [auth H] MOL2 format, chain RA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D]	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 MA [auth G] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	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 AB [auth J] SDF format, chain DB [auth K] SDF format, chain EB [auth K] SDF format, chain FB [auth K] SDF format, chain XA [auth J] SDF format, chain YA [auth J] SDF format, chain ZA [auth J] MOL2 format, chain AB [auth J] MOL2 format, chain DB [auth K] MOL2 format, chain EB [auth K] MOL2 format, chain FB [auth K] MOL2 format, chain XA [auth J] MOL2 format, chain YA [auth J] MOL2 format, chain ZA [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 BA [auth E] SDF format, chain CB [auth K] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain HB [auth L] SDF format, chain IA [auth G] SDF format, chain IB [auth L] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain N [auth A] SDF format, chain QA [auth I] SDF format, chain S [auth B] SDF format, chain TA [auth J] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain HB [auth L] MOL2 format, chain IA [auth G] MOL2 format, chain IB [auth L] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth J] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D]	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
R-Value Work: 0.197
R-Value Observed: 0.199
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

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