3E96 | pdb_00003e96

Crystal structure of dihydrodipicolinate synthase from bacillus clausii

• PDB DOI: https://doi.org/10.2210/pdb3E96/pdb

• Classification: LYASE
• Organism(s): Shouchella clausii KSM-K16
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-21 Released: 2008-09-02 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of dihydrodipicolinate synthase from bacillus clausii

Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.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: 70.51 kDa 
• Atom Count: 5,136 
• Modeled Residue Count: 596 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	316	Shouchella clausii KSM-K16	Mutation(s): 0  Gene Names: ABC3015 EC: 4.2.1.52
UniProt
Find proteins for Q5WDL1 (Shouchella clausii (strain KSM-K16)) Explore Q5WDL1  Go to UniProtKB:  Q5WDL1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.766	α = 90
b = 80.938	β = 90
c = 93.166	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Structure summary
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references