4B5E | pdb_00004b5e

Crystal Structure of an amyloid-beta binding single chain antibody PS2-8

PDB DOI: https://doi.org/10.2210/pdb4B5E/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2012-08-03 Released: 2013-08-21
Deposition Author(s): Beringer, D.X., Dorresteijn, B., Rutten, L., Wienk, H., el Khattabi, M., Kroon-Batenburg, L.M.J., Verrips, C.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.236 (Depositor), 0.242 (DCC)
R-Value Work:
0.181 (Depositor), 0.191 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Amyloid-Beta Binding Single Chain Antibody Ps2-8

Beringer, D.X., Dorresteijn, B., Rutten, L., Wienk, H., El Khattabi, M., Kroon-Batenburg, L.M.J., Verrips, C.T.

To be published.

Macromolecule Content

Total Structure Weight: 27.93 kDa
Atom Count: 2,073
Modeled Residue Count: 253
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PS2-8	A, B	127	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	C [auth A], E [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A]	D [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.236 (Depositor), 0.242 (DCC)
R-Value Work: 0.181 (Depositor), 0.191 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.647	α = 90
b = 59.209	β = 90
c = 133.635	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

Kroon-Batenburg, L.M.J.

Verrips, C.T.

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2017-04-19
Changes: Data collection
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary