7AQL | pdb_00007aql

Crystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (PAI-1) scFv antibody fragment (scFv-33H1F7)

PDB DOI: https://doi.org/10.2210/pdb7AQL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-22 Released: 2021-11-03
Deposition Author(s): Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.224 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (PAI-1) scFv antibody fragment (scFv-33H1F7)

Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 104.57 kDa
Atom Count: 7,705
Modeled Residue Count: 904
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv-33H1F7	A [auth B], B [auth A], C, D	242	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth A] H [auth A] I [auth C] E [auth B], F [auth B], G [auth A], H [auth A], I [auth C], J [auth C], K [auth D], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.224 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.398	α = 90
b = 55.577	β = 90.28
c = 102.493	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	11ZQ918N
Research Foundation - Flanders (FWO)	Belgium	G072915N

Revision History (Full details and data files)

Version 1.0: 2021-11-03
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.