7AE5 | pdb_00007ae5

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form

PDB DOI: https://doi.org/10.2210/pdb7AE5/pdb

Classification: LYASE
Organism(s): Sedimentibacter hydroxybenzoicus
Expression System: Escherichia coli
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: 2.19 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.225 (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: 372.34 kDa
Atom Count: 25,337
Modeled Residue Count: 3,192
Deposited Residue Count: 3,288
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 [auth B] B [auth C] C [auth D] D [auth E] E [auth F] A [auth B], B [auth C], C [auth D], D [auth E], E [auth F], F [auth A]	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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ShdD	G [auth b] H [auth c] I [auth d] J [auth e] K [auth f] G [auth b], H [auth c], I [auth d], J [auth e], K [auth f], L [auth a]	68	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
RB Query on RB Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B] N [auth B] O [auth C] P [auth C] Q [auth D] M [auth B], N [auth B], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth E], U [auth F], V [auth F], W [auth A], X [auth A]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth A] Focus chain X [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth c] SDF format, chain Y [auth b] SDF format, chain DA [auth a] SDF format, chain CA [auth f] SDF format, chain BA [auth e] SDF format, chain AA [auth d] MOL2 format, chain Z [auth c] MOL2 format, chain Y [auth b] MOL2 format, chain DA [auth a] MOL2 format, chain CA [auth f] MOL2 format, chain BA [auth e] MOL2 format, chain AA [auth d] mmCIF format, chain Z [auth c] mmCIF format, chain Y [auth b] mmCIF format, chain DA [auth a] mmCIF format, chain CA [auth f] mmCIF format, chain BA [auth e] mmCIF format, chain AA [auth d]	AA [auth d] BA [auth e] CA [auth f] DA [auth a] Y [auth b] AA [auth d], BA [auth e], CA [auth f], DA [auth a], Y [auth b], Z [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth d] Focus chain BA [auth e] Focus chain CA [auth f] Focus chain DA [auth a] Focus chain Y [auth b] Focus chain Z [auth c] Interactions & Density Focus chain AA [auth d] Focus chain BA [auth e] Focus chain CA [auth f] Focus chain DA [auth a] Focus chain Y [auth b] Focus chain Z [auth c]