4ALB | pdb_00004alb

Structure of Phenolic Acid Decarboxylase from Bacillus subtilis: Tyr19Ala mutant in complex with coumaric acid

PDB DOI: https://doi.org/10.2210/pdb4ALB/pdb

Classification: LYASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-03-02 Released: 2012-08-22
Deposition Author(s): Frank, A., Eborall, W., Hyde, R., Hart, S., Turkenburg, J.P., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free:
0.263 (Depositor), 0.268 (DCC)
R-Value Work:
0.202 (Depositor), 0.204 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Mutational Analysis of Phenolic Acid Decarboxylase from Bacillus Subtilis (Bspad), which Converts Bio-Derived Phenolic Acids to Styrene Derivatives

Frank, A., Eborall, W., Hyde, R., Hart, S., Turkenburg, J.P., Grogan, G.

(2012) Catal Sci Technol 2: 1568

DOI: https://doi.org/10.1039/C2CY20015E

Macromolecule Content

Total Structure Weight: 57.52 kDa
Atom Count: 3,901
Modeled Residue Count: 475
Deposited Residue Count: 483
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENOLIC ACID DECARBOXYLASE PADC	A, B, C	161	Bacillus subtilis	Mutation(s): 1 EC: 4.1.1 (PDB Primary Data), 4.1.1.102 (UniProt)
UniProt
Find proteins for O07006 (Bacillus subtilis (strain 168)) Explore O07006 Go to UniProtKB: O07006
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O07006
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HC4 Query on HC4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	4'-HYDROXYCINNAMIC ACID C₉ H₈ O₃ NGSWKAQJJWESNS-ZZXKWVIFSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.263 (Depositor), 0.268 (DCC)
R-Value Work: 0.202 (Depositor), 0.204 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.21	α = 90
b = 107.21	β = 90
c = 92.8	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Turkenburg, J.P.

Revision History (Full details and data files)

Version 1.0: 2012-08-22
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.