4R1L | pdb_00004r1l

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

PDB DOI: https://doi.org/10.2210/pdb4R1L/pdb

Classification: LIGASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-06 Released: 2014-08-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.213 (Depositor), 0.218 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4R1L

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 206.5 kDa
Atom Count: 14,432
Modeled Residue Count: 1,714
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylacetate-coenzyme A ligase	A, B, C, D	436	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_0428 EC: 6.2.1.30
UniProt
Find proteins for Q8AAN6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAN6 Go to UniProtKB: Q8AAN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8AAN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A]	BA [auth C], H [auth A]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain KA [auth D] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain U [auth B]	F [auth A], KA [auth D], U [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain KA [auth D] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain KA [auth D] Focus chain U [auth B]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain G [auth A]	AA [auth C], G [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain MA [auth D] MOL2 format, chain MA [auth D] mmCIF format, chain MA [auth D]	MA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Interactions & Density Focus chain MA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain V [auth B]	EA [auth C] FA [auth C] M [auth A] N [auth A] NA [auth D] EA [auth C], FA [auth C], M [auth A], N [auth A], NA [auth D], O [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain V [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	E [auth A], JA [auth D], T [auth B], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Z [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	GA [auth C] HA [auth C] IA [auth C] OA [auth D] P [auth A] GA [auth C], HA [auth C], IA [auth C], OA [auth D], P [auth A], PA [auth D], Q [auth A], R [auth A], S [auth A], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth D]	CA [auth C] DA [auth C] I [auth A] J [auth A] K [auth A] CA [auth C], DA [auth C], I [auth A], J [auth A], K [auth A], LA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [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: 2.42 Å
R-Value Free: 0.213 (Depositor), 0.218 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.701	α = 90
b = 211.141	β = 90
c = 71.861	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.