3IN6 | pdb_00003in6

Crystal structure of a fmn-binding protein (swol_0183) from syntrophomonas wolfei subsp. wolfei at 2.12 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IN6/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-11 Released: 2009-08-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal structure of FMN-binding protein (YP_752906.1) from Syntrophomonas wolfei str. Goettingen at 2.12 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.4 kDa 
• Atom Count: 2,407 
• Modeled Residue Count: 294 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-binding protein	A, B	148	Syntrophomonas wolfei subsp. wolfei str. Goettingen G311	Mutation(s): 0  Gene Names: Swol_0183, YP_752906.1
UniProt
Find proteins for Q0B0G9 (Syntrophomonas wolfei subsp. wolfei (strain DSM 2245B / Goettingen)) Explore Q0B0G9  Go to UniProtKB:  Q0B0G9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-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: 2.12 Å
• R-Value Free:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IN6

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.108	α = 90
b = 103.108	β = 90
c = 59.786	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
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, 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
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary