7DVK | pdb_00007dvk

PyrI4 in complex with intermolecular Diels-Alder product

PDB DOI: https://doi.org/10.2210/pdb7DVK/pdb

Classification: ISOMERASE
Organism(s): Streptomyces rugosporus
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: 2.60 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 83.91 kDa
Atom Count: 5,054
Modeled Residue Count: 652
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spiro-conjugate synthase	A, B, C, D	194	Streptomyces rugosporus	Mutation(s): 0 Gene Names: pyrI4 EC: 5.5.1 (PDB Primary Data), 5 (UniProt)
UniProt
Find proteins for K7QVW7 (Streptomyces rugosporus) Explore K7QVW7 Go to UniProtKB: K7QVW7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K7QVW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HOF (Subject of Investigation/LOI) Query on HOF Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	methyl 4-[[(1S,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamoyloxymethyl]benzoate C₁₉ H₂₄ N₂ O₅ VSPPPQJKRCRPEW-HOTGVXAUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.272 (Depositor), 0.270 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.959	α = 90
b = 102.959	β = 90
c = 168.798	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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