3IOY | pdb_00003ioy

Structure of putative short-chain dehydrogenase (Saro_0793) from Novosphingobium aromaticivorans

• PDB DOI: https://doi.org/10.2210/pdb3IOY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-08-15 Released: 2010-01-19 
• Deposition Author(s): Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Structure of putative short-chain dehydrogenase (Saro_0793) from Novosphingobium aromaticivorans

Ramagopal, U.A., Morano, C., Burley, S.K., 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: 69.84 kDa 
• Atom Count: 4,245 
• Modeled Residue Count: 547 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	319	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 2  Gene Names: Saro_0793
UniProt
Find proteins for Q2GA85 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GA85  Go to UniProtKB:  Q2GA85

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.683	α = 90
b = 100.753	β = 101.91
c = 63.463	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Ramagopal, U.A., Morano, C., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references
• Version 1.5: 2024-02-21
  Changes: Data collection