3FKD | pdb_00003fkd

The crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb3FKD/pdb

• Classification: LYASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-16 Released: 2009-02-03 
• Deposition Author(s): Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

The crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas gingivalis

Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 161.83 kDa 
• Atom Count: 10,610 
• Modeled Residue Count: 1,286 
• Deposited Residue Count: 1,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine-O-3-phosphate decarboxylase	A, B, C, D	350	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: PG_0012
UniProt
Find proteins for Q7MXY2 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXY2  Go to UniProtKB:  Q7MXY2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.443	α = 90
b = 101.513	β = 90.22
c = 93.714	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Zhang, Z., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-11-13
  Changes: Derived calculations, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Structure summary