8AHZ

Native VirD of Streptomyces virginiae

PDB DOI: 10.2210/pdb8AHZ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces virginiae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-07-25 Released: 2023-03-15
Deposition Author(s): Collin, S., Gruez, A.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.180
R-Value Work: 0.159
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Decrypting the programming of beta-methylation in virginiamycin M biosynthesis

Collin, S., Gruez, A.

(2023) Nat Commun

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase	A, B, C	250	Streptomyces virginiae	Mutation(s): 0 Gene Names: virD
UniProt
Find proteins for A4PHM7 (Streptomyces virginiae) Explore A4PHM7 Go to UniProtKB: A4PHM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4PHM7
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain G [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain R [auth A] SDF format, chain U [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth B]	AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain QA [auth C] SDF format, chain T [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain T [auth A]	FA [auth B], QA [auth C], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.180
R-Value Work: 0.159
R-Value Observed: 0.160
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.31	α = 90
b = 84.31	β = 90
c = 230.19	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Collin, S.

Gruez, A.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-11-JSV8-003-01
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE92-0006-01
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE93-0002-01