7DVI

Crystal Structure of AbnU: An exo-specific intermolecular Diels-Alderase

PDB DOI: https://doi.org/10.2210/pdb7DVI/pdb

Classification: ISOMERASE
Organism(s): Parafrankia colletiae
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2021-01-13 Released: 2021-08-18
Deposition Author(s): Kashyap, R., Addlagatta, A.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR), Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates.

Kashyap, R., Yerra, N.V., Oja, J., Bala, S., Potuganti, R., Thota, J.R., Alla, M., Pal, D., Addlagatta, A.

(2021) Commun Chem

DOI: https://doi.org/10.1038/s42004-021-00552-9

Macromolecule Content

Total Structure Weight: 18.45 kDa
Atom Count: 1,255
Modelled Residue Count: 134
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AOC_like domain-containing protein	A	151	Parafrankia colletiae	Mutation(s): 0 Gene Names: CC117_14200
UniProt
Find proteins for A0A1S1R073 (Parafrankia colletiae) Explore A0A1S1R073 Go to UniProtKB: A0A1S1R073
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1S1R073
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A]	W [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] 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 S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] 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 S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], 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], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] 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 Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] 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 Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.437	α = 90
b = 104.437	β = 90
c = 67.661	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Kashyap, R.

Addlagatta, A.

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	33/2018/MD-FTT&FTC-ANB
Science and Engineering Research Board (SERB)	India	EMR/2015/000461
Science and Engineering Research Board (SERB)	India	CRG/2019/006013