3EBY | pdb_00003eby

Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EBY/pdb

• Classification: structural genomics, unknown function
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-28 Released: 2008-09-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 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)

Macromolecule Content 

• Total Structure Weight: 18.15 kDa 
• Atom Count: 1,412 
• Modeled Residue Count: 153 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase	A	163	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: YP_001165631.1, Saro_3860
UniProt
Find proteins for A4XDU4 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XDU4  Go to UniProtKB:  A4XDU4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EBY

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.29	α = 90
b = 80.29	β = 90
c = 145.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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