4RVO

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

DOI: 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
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

This is version 1.2 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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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
Find proteins for Q8AAN6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)) Explore Q8AAN6 Go to UniProtKB: Q8AAN6
Protein Feature View 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 [A] SDF format, chain FA [C] SDF format, chain OA [D] SDF format, chain W [B] MOL2 format, chain F [A] MOL2 format, chain FA [C] MOL2 format, chain OA [D] MOL2 format, chain W [B]	A, B, C, D	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain N [A] MOL2 format, chain N [A]	A	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain KA [C] SDF format, chain P [A] MOL2 format, chain KA [C] MOL2 format, chain P [A]	A, C	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [B] SDF format, chain O [A] MOL2 format, chain AA [B] MOL2 format, chain O [A]	A, B	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain JA [C] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [A] SDF format, chain SA [D] SDF format, chain Y [B] SDF format, chain Z [B] MOL2 format, chain JA [C] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [A] MOL2 format, chain SA [D] MOL2 format, chain Y [B] MOL2 format, chain Z [B]	A, B, C, D	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain EA [C] SDF format, chain PA [D] SDF format, chain V [B] MOL2 format, chain E [A] MOL2 format, chain EA [C] MOL2 format, chain PA [D] MOL2 format, chain V [B]	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [B] SDF format, chain CA [B] SDF format, chain DA [B] SDF format, chain LA [C] SDF format, chain MA [C] SDF format, chain NA [C] SDF format, chain Q [A] SDF format, chain R [A] SDF format, chain S [A] SDF format, chain T [A] SDF format, chain TA [D] SDF format, chain U [A] SDF format, chain UA [D] SDF format, chain VA [D] MOL2 format, chain BA [B] MOL2 format, chain CA [B] MOL2 format, chain DA [B] MOL2 format, chain LA [C] MOL2 format, chain MA [C] MOL2 format, chain NA [C] MOL2 format, chain Q [A] MOL2 format, chain R [A] MOL2 format, chain S [A] MOL2 format, chain T [A] MOL2 format, chain TA [D] MOL2 format, chain U [A] MOL2 format, chain UA [D] MOL2 format, chain VA [D]	A, B, C, D	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain GA [C] SDF format, chain H [A] SDF format, chain HA [C] SDF format, chain I [A] SDF format, chain QA [D] MOL2 format, chain G [A] MOL2 format, chain GA [C] MOL2 format, chain H [A] MOL2 format, chain HA [C] MOL2 format, chain I [A] MOL2 format, chain QA [D]	A, C, D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
UNL Query on UNL Download Ideal Coordinates CCD File SDF format, chain IA [C] SDF format, chain J [A] SDF format, chain RA [D] SDF format, chain X [B] MOL2 format, chain IA [C] MOL2 format, chain J [A] MOL2 format, chain RA [D] MOL2 format, chain X [B]	A, B, C, D	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction

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
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2
Diffraction Data DOI: 10.18430/M3VP43 Protein Diffraction

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