4R1M | pdb_00004r1m

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 A resolution

PDB DOI: https://doi.org/10.2210/pdb4R1M/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: 2.48 Å
R-Value Free:
0.200 (Depositor), 0.207 (DCC)
R-Value Work:
0.175 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.48 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 203.21 kDa
Atom Count: 13,860
Modeled Residue Count: 1,720
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain F [auth A] SDF format, chain DA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain DA [auth D]	DA [auth D], F [auth A], R [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain DA [auth D] Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain DA [auth D] Focus chain F [auth A] Focus chain R [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth D]	CA [auth D], E [auth A], Q [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain Q [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain Q [auth B] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain T [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain T [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain T [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] EA [auth D] FA [auth D] H [auth A] AA [auth C], BA [auth C], EA [auth D], FA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], T [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C]	X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain X [auth C] Focus chain Y [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain S [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain S [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain S [auth B] mmCIF format, chain G [auth A]	G [auth A], S [auth B], V [auth C], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C]

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: 2.48 Å
R-Value Free: 0.200 (Depositor), 0.207 (DCC)
R-Value Work: 0.175 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.06	α = 90
b = 211.87	β = 90
c = 72.25	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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: 2023-11-29
Changes: Data collection, Database references
Version 1.6: 2024-11-20
Changes: 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.