2EEO | pdb_00002eeo

Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase Complexed with Fumarate

• PDB DOI: https://doi.org/10.2210/pdb2EEO/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-16 Released: 2008-02-19 
• Deposition Author(s): Goto, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.25 kDa 
• Atom Count: 1,047 
• Modeled Residue Count: 118 
• Deposited Residue Count: 119 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate 1-decarboxylase	A	24	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.1.1.11
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
Aspartate 1-decarboxylase	B	95	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.1.1.11
UniProt
Find proteins for Q5SKN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKN7  Go to UniProtKB:  Q5SKN7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUM	D [auth B]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N
PYR	C [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.118	α = 90
b = 68.118	β = 90
c = 48.562	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Goto, M.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2012-02-15
  Changes: Non-polymer description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations