7AE4

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

PDB DOI: https://doi.org/10.2210/pdb7AE4/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: 3.31 Å
R-Value Free: 0.198
R-Value Work: 0.163
R-Value Observed: 0.165

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: 373.29 kDa
Atom Count: 25,697
Modelled Residue Count: 3,257
Deposited Residue Count: 3,288
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9S4M7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4R102
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain M [auth A] SDF format, chain NA [auth E] SDF format, chain PA [auth E] SDF format, chain VA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain VA [auth F]	AA [auth C] GA [auth D] M [auth A] NA [auth E] PA [auth E] AA [auth C], GA [auth D], M [auth A], NA [auth E], PA [auth E], VA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain M [auth A] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain VA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain M [auth A] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain VA [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain JA [auth D] SDF format, chain Q [auth A] SDF format, chain TA [auth E] SDF format, chain X [auth B] SDF format, chain YA [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain YA [auth F]	DA [auth C] JA [auth D] Q [auth A] TA [auth E] X [auth B] DA [auth C], JA [auth D], Q [auth A], TA [auth E], X [auth B], YA [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth C] Focus chain JA [auth D] Focus chain Q [auth A] Focus chain TA [auth E] Focus chain X [auth B] Focus chain YA [auth F] Interactions & Density Focus chain DA [auth C] Focus chain JA [auth D] Focus chain Q [auth A] Focus chain TA [auth E] Focus chain X [auth B] Focus chain YA [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth a] SDF format, chain BB [auth b] SDF format, chain CB [auth c] SDF format, chain DB [auth d] SDF format, chain EB [auth e] SDF format, chain FB [auth f] MOL2 format, chain AB [auth a] MOL2 format, chain BB [auth b] MOL2 format, chain CB [auth c] MOL2 format, chain DB [auth d] MOL2 format, chain EB [auth e] MOL2 format, chain FB [auth f]	AB [auth a] BB [auth b] CB [auth c] DB [auth d] EB [auth e] AB [auth a], BB [auth b], CB [auth c], DB [auth d], EB [auth e], FB [auth f]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth a] Focus chain BB [auth b] Focus chain CB [auth c] Focus chain DB [auth d] Focus chain EB [auth e] Focus chain FB [auth f] Interactions & Density Focus chain AB [auth a] Focus chain BB [auth b] Focus chain CB [auth c] Focus chain DB [auth d] Focus chain EB [auth e] Focus chain FB [auth f]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain OA [auth E] MOL2 format, chain OA [auth E]	OA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain OA [auth E] Interactions & Density Focus chain OA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Z [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Z [auth B]	FA [auth C] LA [auth D] MA [auth D] S [auth A] T [auth A] FA [auth C], LA [auth D], MA [auth D], S [auth A], T [auth A], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain KA [auth D] SDF format, chain R [auth A] SDF format, chain UA [auth E] SDF format, chain Y [auth B] SDF format, chain ZA [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth F]	EA [auth C] KA [auth D] R [auth A] UA [auth E] Y [auth B] EA [auth C], KA [auth D], R [auth A], UA [auth E], Y [auth B], ZA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain KA [auth D] Focus chain R [auth A] Focus chain UA [auth E] Focus chain Y [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain EA [auth C] Focus chain KA [auth D] Focus chain R [auth A] Focus chain UA [auth E] Focus chain Y [auth B] Focus chain ZA [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain XA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F]	BA [auth C] CA [auth C] HA [auth D] IA [auth D] N [auth A] BA [auth C], CA [auth C], HA [auth D], IA [auth D], N [auth A], O [auth A], P [auth A], QA [auth E], RA [auth E], SA [auth E], U [auth B], V [auth B], W [auth B], WA [auth F], XA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth F] Focus chain XA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth F] Focus chain XA [auth F]