3EDO | pdb_00003edo

Crystal structure of Flavoprotein in Complex with FMN (YP_193882.1) from Lactobacillus acidophilus NCFM at 1.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EDO/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Lactobacillus acidophilus NCFM
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-03 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: 1.20 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Crystal structure of Flavoprotein in Complex with FMN (YP_193882.1) from Lactobacillus acidophilus NCFM at 1.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.97 kDa 
• Atom Count: 3,248 
• Modeled Residue Count: 300 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative trp repressor binding protein	A, B	151	Lactobacillus acidophilus NCFM	Mutation(s): 0  Gene Names: YP_193882.1, LBA1001
UniProt
Find proteins for Q5FKC3 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FKC3  Go to UniProtKB:  Q5FKC3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
MSO	A, B	L-PEPTIDE LINKING	C5 H11 N O3 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EDO

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.56	α = 90
b = 52.03	β = 90
c = 156.75	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: 2008-09-30 
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: 2017-10-25
  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