4RVO | pdb_00004rvo

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution

PDB DOI: https://doi.org/10.2210/pdb4RVO/pdb
Entry: 4RVO supersedes: 4R1W

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

Deposited: 2014-11-26 Released: 2014-12-31
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.214 (Depositor), 0.231 (DCC)
R-Value Work:
0.187 (Depositor), 0.206 (DCC)
R-Value Observed:
0.189 (Depositor)

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 Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 205.27 kDa
Atom Count: 14,424
Modeled Residue Count: 1,724
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain W [auth B] SDF format, chain OA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain OA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain OA [auth D]	F [auth A], FA [auth C], OA [auth D], W [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth C] Focus chain OA [auth D] Focus chain W [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain P [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain P [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain P [auth A]	KA [auth C], P [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain KA [auth C] Focus chain P [auth A] Interactions & Density Focus chain KA [auth C] Focus chain P [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain O [auth A]	AA [auth B], O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain O [auth A] Interactions & Density Focus chain AA [auth B] Focus chain O [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain SA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain K [auth A]	JA [auth C] K [auth A] L [auth A] M [auth A] SA [auth D] JA [auth C], K [auth A], L [auth A], M [auth A], SA [auth D], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain SA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain SA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain PA [auth D] SDF format, chain V [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain V [auth B]	E [auth A], EA [auth C], PA [auth D], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth C] Focus chain PA [auth D] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth C] Focus chain PA [auth D] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain Q [auth A] SDF format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain DA [auth B]	BA [auth B] CA [auth B] DA [auth B] LA [auth C] MA [auth C] BA [auth B], CA [auth B], DA [auth B], LA [auth C], MA [auth C], NA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], TA [auth D], U [auth A], UA [auth D], VA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain VA [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain QA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C]	G [auth A] GA [auth C] H [auth A] HA [auth C] I [auth A] G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], QA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain QA [auth D] Interactions & Density Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain QA [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	IA [auth C], J [auth A], RA [auth D], X [auth B]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain J [auth A] Focus chain RA [auth D] Focus chain X [auth B] Interactions & Density Focus chain IA [auth C] Focus chain J [auth A] Focus chain RA [auth D] Focus chain X [auth B]

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: 2.41 Å
R-Value Free: 0.214 (Depositor), 0.231 (DCC)
R-Value Work: 0.187 (Depositor), 0.206 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.237	α = 90
b = 210.223	β = 90
c = 71.504	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

This entry supersedes: 4R1W

Revision History (Full details and data files)

Version 1.0: 2014-12-31
Type: Initial release
Version 1.1: 2015-03-18
Changes: Advisory
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary