6XYF | pdb_00006xyf

Nanobody 22

PDB DOI: https://doi.org/10.2210/pdb6XYF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-01-30 Released: 2021-02-10
Deposition Author(s): Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free:
0.153 (Depositor), 0.153 (DCC)
R-Value Work:
0.125 (Depositor), 0.126 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Engineered nanobodies with a lanthanide binding motif for crystallographic phasing

Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

To be published.

Macromolecule Content

Total Structure Weight: 14.3 kDa
Atom Count: 1,179
Modeled Residue Count: 125
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 22	A	132	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free: 0.153 (Depositor), 0.153 (DCC)
R-Value Work: 0.125 (Depositor), 0.126 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.322	α = 90
b = 38.685	β = 98.271
c = 44.873	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary