3FDJ | pdb_00003fdj

The structure of a DegV family protein from Eubacterium eligens.

• PDB DOI: https://doi.org/10.2210/pdb3FDJ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Lachnospira eligens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-25 Released: 2009-02-03 
• Deposition Author(s): Cuff, M.E., Hendricks, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5UXY

Literature

The structure of a DegV family protein from Eubacterium eligens.

Cuff, M.E., Hendricks, R., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.36 kDa 
• Atom Count: 2,530 
• Modeled Residue Count: 276 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegV family protein	A	278	Lachnospira eligens	Mutation(s): 0  Gene Names: ASSEMBLY.20070618:0-0:0-0 (zvnW5vjFOAACMF8NLOPRFTmWH60:01:1-275)
UniProt
Find proteins for D0VX07 (Lachnospira eligens) Explore D0VX07  Go to UniProtKB:  D0VX07

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	B [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	F [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.80 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.445	α = 90
b = 57.445	β = 90
c = 186.558	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Cuff, M.E., Hendricks, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Structure summary