2EHH | pdb_00002ehh

Crystal structure of dihydrodipicolinate synthase from aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2EHH/pdb

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


• Deposited: 2007-03-06 Released: 2007-05-01 
• Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydrodipicolinate synthase from aquifex aeolicus

Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 131.03 kDa 
• Atom Count: 9,591 
• Modeled Residue Count: 1,174 
• Deposited Residue Count: 1,176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B [auth C], C [auth D], D [auth E]	294	Aquifex aeolicus	Mutation(s): 0  Gene Names: AQ_1143 EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for O67216 (Aquifex aeolicus (strain VF5)) Explore O67216  Go to UniProtKB:  O67216

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.321	α = 90
b = 146.953	β = 109.35
c = 97.877	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Kumarevel, T.S., Karthe, P., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary