3D0C | pdb_00003d0c

Crystal structure of dihydrodipicolinate synthase from Oceanobacillus iheyensis at 1.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D0C/pdb

• Classification: LYASE
• Organism(s): Oceanobacillus iheyensis HTE831
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-01 Released: 2008-05-13 
• Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of dihydrodipicolinate synthase from Oceanobacillus iheyensis at 1.9 A resolution.

Satyanarayana, L., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, 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)

Macromolecule Content 

• Total Structure Weight: 70.3 kDa 
• Atom Count: 5,147 
• Modeled Residue Count: 602 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	314	Oceanobacillus iheyensis HTE831	Mutation(s): 1  Gene Names: OB2845, DHDPS EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q8EMJ7 (Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831)) Explore Q8EMJ7  Go to UniProtKB:  Q8EMJ7

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: 1.90 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.037	α = 90
b = 57.063	β = 90
c = 71.457	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXCD	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary