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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.191 (Depositor), 0.204 (DCC)
R-Value Work:
0.160 (Depositor), 0.169 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VX07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.204 (DCC)
R-Value Work: 0.160 (Depositor), 0.169 (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

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Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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