4RVN | pdb_00004rvn

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb4RVN/pdb
Entry: 4RVN supersedes: 4R1X

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

Deposited: 2014-11-26 Released: 2015-01-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.219 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 205.4 kDa
Atom Count: 14,520
Modeled Residue Count: 1,717
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8AAN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Z [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain G [auth A] mmCIF format, chain Z [auth C]	G [auth A], Z [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain G [auth A] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain Z [auth C]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain JA [auth D] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain F [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C]	F [auth A], JA [auth D], T [auth B], Y [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain F [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	EA [auth C], L [auth A], LA [auth D], M [auth A], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [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 IA [auth D] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C]	E [auth A], IA [auth D], S [auth B], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain X [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain W [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain W [auth B]	FA [auth C] GA [auth C] HA [auth C] MA [auth D] N [auth A] FA [auth C], GA [auth C], HA [auth C], MA [auth D], N [auth A], NA [auth D], O [auth A], P [auth A], Q [auth A], R [auth A], W [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain W [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	AA [auth C] BA [auth C] CA [auth C] H [auth A] I [auth A] AA [auth C], BA [auth C], CA [auth C], H [auth A], I [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	DA [auth C], K [auth A], KA [auth D], U [auth B]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain U [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: 2.20 Å
R-Value Free: 0.219 (Depositor), 0.230 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34RVN

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.78	α = 90
b = 211.3	β = 90
c = 71.98	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

This entry supersedes: 4R1X

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2015-03-18
Changes: Advisory
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-27
Changes: Structure summary