3DDE

Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DDE/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Shewanella denitrificans OS217
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-05 Released: 2008-06-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Literature

Crystal structure of Domain of Unknown Function with a Heme Oxygenase-like Fold (YP_564736.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 55.35 kDa 
• Atom Count: 3,753 
• Modelled Residue Count: 463 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold	A, B	239	Shewanella denitrificans OS217	Mutation(s): 0  Gene Names: YP_564736.1, Sden_3740
UniProt
Find proteins for Q12HR3 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12HR3  Go to UniProtKB:  Q12HR3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A], D [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	E [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-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: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M33DDE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.81	α = 90
b = 66	β = 90
c = 84.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
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: 2008-06-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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