4OJD

Crystal structure of a C-terminally truncated trimeric ectodomain of the C. elegans fusion protein EFF-1 G260A/D321E/D322E mutant

PDB DOI: https://doi.org/10.2210/pdb4OJD/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Caenorhabditis elegans
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2014-01-21 Released: 2014-05-14
Deposition Author(s): Krey, T., Rey, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.222
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 60.11 kDa
Atom Count: 3,684
Modelled Residue Count: 444
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EFF-1A	A [auth H]	526	Caenorhabditis elegans	Mutation(s): 3 Gene Names: C26D10.5, CELE_C26D10.5, eff-1
UniProt
Find proteins for G5ECA1 (Caenorhabditis elegans) Explore G5ECA1 Go to UniProtKB: G5ECA1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5ECA1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A]	3		N-Glycosylation	Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H]	C [auth H], D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Interactions & Density Focus chain C [auth H] Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.222
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.443	α = 90
b = 132.443	β = 90
c = 132.443	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Krey, T.

Rey, F.A.

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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4OJD

Crystal structure of a C-terminally truncated trimeric ectodomain of the C. elegans fusion protein EFF-1 G260A/D321E/D322E mutant

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)