3N05 | pdb_00003n05

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM STREPTOMYCES AVERMITILIS

• PDB DOI: https://doi.org/10.2210/pdb3N05/pdb

• Classification: LIGASE
• Organism(s): Streptomyces avermitilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-13 Released: 2010-07-07 
• Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Do, J., Sauder, J.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.268 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal Structure of Nh3-Dependent Nad+ Synthetase from Streptomyces Avermitilis

Patskovsky, Y., Toro, R., Freeman, J., Do, J., Sauder, J.M., Gerlt, J.A., 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: 128.33 kDa 
• Atom Count: 8,755 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NH(3)-dependent NAD(+) synthetase	A, B	590	Streptomyces avermitilis	Mutation(s): 0  Gene Names: nadE, SAV5948, SAV_5948 EC: 6.3.5.1
UniProt
Find proteins for Q82AV7 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82AV7  Go to UniProtKB:  Q82AV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.268 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.628	α = 90
b = 108.771	β = 90
c = 126.643	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Patskovsky, Y., Toro, R., Freeman, J., Do, J., Sauder, J.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references