2P3E | pdb_00002p3e

Crystal structure of AQ1208 from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2P3E/pdb

• Classification: LYASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-08 Released: 2007-05-01 
• Deposition Author(s): Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

To be Published

Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.-C.

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)

Macromolecule Content 

• Total Structure Weight: 94.05 kDa 
• Atom Count: 6,860 
• Modeled Residue Count: 801 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A, B	420	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: lysA, aq_1208 EC: 4.1.1.20
UniProt
Find proteins for O67262 (Aquifex aeolicus (strain VF5)) Explore O67262  Go to UniProtKB:  O67262

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.515	α = 90
b = 87.675	β = 90
c = 152.581	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Zhu, J., Swindell II, J.T., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Fu, Z.-Q., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description