2P8G | pdb_00002p8g

Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2P8G/pdb

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


• Deposited: 2007-03-22 Released: 2007-04-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.146 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.02 kDa 
• Atom Count: 1,673 
• Modeled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenolic acid decarboxylase	A	162	Bacillus subtilis	Mutation(s): 8  Gene Names: padC, pad, BSU34400 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.146 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32P8G

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.475	α = 90
b = 117.475	β = 90
c = 117.475	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-01-25
  Changes: Database references
• Version 1.6: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.7: 2023-11-15
  Changes: Data collection
• Version 1.8: 2024-11-13
  Changes: Structure summary