3E39 | pdb_00003e39

Crystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3E39/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oleidesulfovibrio alaskensis G20
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-06 Released: 2008-08-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of Putative Nitroreductase in Complex with FMN (YP_387283.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

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: 40.45 kDa 
• Atom Count: 3,179 
• Modeled Residue Count: 347 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Nitroreductase	A, B	178	Oleidesulfovibrio alaskensis G20	Mutation(s): 0  Gene Names: YP_387283.1, Dde_0787
UniProt
Find proteins for Q314Q8 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q314Q8  Go to UniProtKB:  Q314Q8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], G [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PGE	H [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.70 Å
• R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33E39

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.78	α = 90
b = 67.99	β = 90
c = 99.74	γ = 90

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: 2008-08-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary