7AE7 | pdb_00007ae7

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form, with truncated ShVdcD (V59X)

PDB DOI: https://doi.org/10.2210/pdb7AE7/pdb

Classification: LYASE
Organism(s): Sedimentibacter hydroxybenzoicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-17 Released: 2021-08-25
Deposition Author(s): Marshall, S.A., Leys, D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Domain mobility and allosteric activation of UbiD decarboxylases

Marshall, S.A., Payne, K.A.P., Leys, D.

To be published.

Macromolecule Content

Total Structure Weight: 364.92 kDa
Atom Count: 24,349
Modeled Residue Count: 3,146
Deposited Residue Count: 3,228
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenolic acid decarboxylase	A, B, C, D, E A, B, C, D, E, F	480	Sedimentibacter hydroxybenzoicus	Mutation(s): 0 Gene Names: shdC, ohb1 EC: 4.1.1.63 (PDB Primary Data), 4.1.1.61 (PDB Primary Data)
UniProt
Find proteins for Q9S4M7 (Sedimentibacter hydroxybenzoicus) Explore Q9S4M7 Go to UniProtKB: Q9S4M7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S4M7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ShdD	G [auth a] H [auth b] I [auth c] J [auth d] K [auth e] G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], L [auth f]	58	Sedimentibacter hydroxybenzoicus	Mutation(s): 0 Gene Names: shdD
UniProt
Find proteins for Q4R102 (Sedimentibacter hydroxybenzoicus) Explore Q4R102 Go to UniProtKB: Q4R102
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4R102
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth f] SDF format, chain V [auth e] SDF format, chain U [auth d] SDF format, chain T [auth c] SDF format, chain S [auth b] SDF format, chain R [auth a] MOL2 format, chain W [auth f] MOL2 format, chain V [auth e] MOL2 format, chain U [auth d] MOL2 format, chain T [auth c] MOL2 format, chain S [auth b] MOL2 format, chain R [auth a] mmCIF format, chain W [auth f] mmCIF format, chain V [auth e] mmCIF format, chain U [auth d] mmCIF format, chain T [auth c] mmCIF format, chain S [auth b] mmCIF format, chain R [auth a]	R [auth a] S [auth b] T [auth c] U [auth d] V [auth e] R [auth a], S [auth b], T [auth c], U [auth d], V [auth e], W [auth f]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth a] Focus chain S [auth b] Focus chain T [auth c] Focus chain U [auth d] Focus chain V [auth e] Focus chain W [auth f] Interactions & Density Focus chain R [auth a] Focus chain S [auth b] Focus chain T [auth c] Focus chain U [auth d] Focus chain V [auth e] Focus chain W [auth f]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A], N [auth B], O [auth C], P [auth E], Q [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth F]