3EF8 | pdb_00003ef8

Crystal structure of Putative Scytalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EF8/pdb

• Classification: LYASE
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-08 Released: 2008-09-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of Putative Scyalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 37.08 kDa 
• Atom Count: 2,797 
• Modeled Residue Count: 298 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Scyalone Dehydratase	A, B	150	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: YP_496742.1, Saro_1465
UniProt
Find proteins for Q2G8B5 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2G8B5  Go to UniProtKB:  Q2G8B5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	K [auth A], N [auth B], O [auth B], P [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A], H [auth A], I [auth A], J [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], E [auth A], F [auth A], L [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 1.50 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EF8

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.851	α = 90
b = 59.851	β = 90
c = 237.504	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-09-13
  Changes: Refinement description, Structure summary
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Structure summary