7AE4 | pdb_00007ae4

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 (Depositor), 0.199 (DCC)
R-Value Work:
0.163 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (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: 373.29 kDa
Atom Count: 25,697
Modeled Residue Count: 3,257
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, 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]	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain VA [auth F] SDF format, chain PA [auth E] SDF format, chain NA [auth E] SDF format, chain M [auth A] SDF format, chain GA [auth D] SDF format, chain AA [auth C] MOL2 format, chain VA [auth F] MOL2 format, chain PA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain VA [auth F] mmCIF format, chain PA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain AA [auth C]	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 YA [auth F] SDF format, chain X [auth B] SDF format, chain TA [auth E] SDF format, chain Q [auth A] SDF format, chain JA [auth D] SDF format, chain DA [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain DA [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain DA [auth C]	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 FB [auth f] SDF format, chain EB [auth e] SDF format, chain DB [auth d] SDF format, chain CB [auth c] SDF format, chain BB [auth b] SDF format, chain AB [auth a] MOL2 format, chain FB [auth f] MOL2 format, chain EB [auth e] MOL2 format, chain DB [auth d] MOL2 format, chain CB [auth c] MOL2 format, chain BB [auth b] MOL2 format, chain AB [auth a] mmCIF format, chain FB [auth f] mmCIF format, chain EB [auth e] mmCIF format, chain DB [auth d] mmCIF format, chain CB [auth c] mmCIF format, chain BB [auth b] mmCIF format, chain AB [auth a]	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] mmCIF 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 Z [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain MA [auth D] SDF format, chain LA [auth D] SDF format, chain FA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain FA [auth C]	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 ZA [auth F] SDF format, chain Y [auth B] SDF format, chain UA [auth E] SDF format, chain R [auth A] SDF format, chain KA [auth D] SDF format, chain EA [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain EA [auth C] mmCIF format, chain ZA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain EA [auth C]	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 XA [auth F] SDF format, chain WA [auth F] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain SA [auth E] SDF format, chain RA [auth E] SDF format, chain QA [auth E] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	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]