1VC3 | pdb_00001vc3

Crystal Structure of L-Aspartate-alpha-Decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb1VC3/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-04 Released: 2005-06-28 
• Deposition Author(s): Nakajima, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 

Literature

Crystal Structure of L-Aspartate-alpha-Decarboxylase

Goto, M., Omi, R., Nakajima, O., Miyahara, I., Hirotsu, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.11 kDa 
• Atom Count: 1,071 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-Aspartate-alpha-Decarboxylase light chain	A	24	Thermus thermophilus	Mutation(s): 0  Gene Names: HB8 EC: 4.1.1.1 (PDB Primary Data), 4.1.1.11 (UniProt)
UniProt
Find proteins for Q5SKN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKN7  Go to UniProtKB:  Q5SKN7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-Aspartate-alpha-Decarboxylase heavy chain	B	96	Thermus thermophilus	Mutation(s): 0  Gene Names: HB8 EC: 4.1.1.1 (PDB Primary Data), 4.1.1.11 (UniProt)
UniProt
Find proteins for Q5SKN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKN7  Go to UniProtKB:  Q5SKN7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.215 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.53	α = 90
b = 67.53	β = 90
c = 47.8	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Nakajima, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-11-20
  Changes: Structure summary