2Z0I

Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus

• PDB DOI: https://doi.org/10.2210/pdb2Z0I/pdb

• Classification: LYASE
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2007-05-07 Released: 2008-05-13 
• Deposition Author(s): Wang, H., Xie, Y., Kawazoe, M., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus

Wang, H., Xie, Y., Kawazoe, M., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, 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: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.1 kDa 
• Atom Count: 4,347 
• Modelled Residue Count: 559 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta-aminolevulinic acid dehydratase	A, B	330	Mus musculus	Mutation(s): 0  EC: 4.2.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for P10518 (Mus musculus) Explore P10518  Go to UniProtKB:  P10518
IMPC:  MGI:96853

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.51	α = 90
b = 121.51	β = 90
c = 196.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Wang, H., Xie, Y., Kawazoe, M., Kishishita, S., Murayama, K., Takemoto, C., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary