7ORX | pdb_00007orx

Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase

PDB DOI: https://doi.org/10.2210/pdb7ORX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-06 Released: 2021-06-16
Deposition Author(s): Wilkinson, R.C., Fulop, V.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.233 (Depositor), 0.225 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from

Wei, Z., Wilkinson, R.C., Rashid, G.M.M., Brown, D., Fulop, V., Bugg, T.D.H.

(2019) Biochemistry 58: 5281-5293

DOI: https://doi.org/10.1021/acs.biochem.9b00177

Macromolecule Content

Total Structure Weight: 223.89 kDa
Atom Count: 15,727
Modeled Residue Count: 2,112
Deposited Residue Count: 2,124
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable benzoylformate decarboxylase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	531	Rhodococcus jostii RHA1	Mutation(s): 0 Gene Names: RHA1_ro02985 EC: 4.1.1.7 (PDB Primary Data), 2.2.1.6 (UniProt)
UniProt
Find proteins for Q0SCE8 (Rhodococcus jostii (strain RHA1)) Explore Q0SCE8 Go to UniProtKB: Q0SCE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0SCE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download:Ideal Coordinates CCD File SDF format, chain K [auth DDD] SDF format, chain I [auth CCC] SDF format, chain G [auth BBB] SDF format, chain E [auth AAA] MOL2 format, chain K [auth DDD] MOL2 format, chain I [auth CCC] MOL2 format, chain G [auth BBB] MOL2 format, chain E [auth AAA] mmCIF format, chain K [auth DDD] mmCIF format, chain I [auth CCC] mmCIF format, chain G [auth BBB] mmCIF format, chain E [auth AAA]	E [auth AAA], G [auth BBB], I [auth CCC], K [auth DDD]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain E [auth AAA] Focus chain G [auth BBB] Focus chain I [auth CCC] Focus chain K [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain G [auth BBB] Focus chain I [auth CCC] Focus chain K [auth DDD]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth DDD] SDF format, chain J [auth CCC] SDF format, chain H [auth BBB] SDF format, chain F [auth AAA] MOL2 format, chain L [auth DDD] MOL2 format, chain J [auth CCC] MOL2 format, chain H [auth BBB] MOL2 format, chain F [auth AAA] mmCIF format, chain L [auth DDD] mmCIF format, chain J [auth CCC] mmCIF format, chain H [auth BBB] mmCIF format, chain F [auth AAA]	F [auth AAA], H [auth BBB], J [auth CCC], L [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain J [auth CCC] Focus chain L [auth DDD] Interactions & Density Focus chain F [auth AAA] Focus chain H [auth BBB] Focus chain J [auth CCC] Focus chain L [auth DDD]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.233 (Depositor), 0.225 (DCC)
R-Value Work: 0.195 (Depositor)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.5	α = 90
b = 132.24	β = 90
c = 138.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-16

Deposition Author(s):

Wilkinson, R.C.

Fulop, V.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M025772/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M003523/1

Revision History (Full details and data files)

Version 1.0: 2021-06-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary