6ROD | pdb_00006rod

Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation

PDB DOI: https://doi.org/10.2210/pdb6ROD/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-05-11 Released: 2020-06-03
Deposition Author(s): Wan, M., Ronzoni, R., Lomas, D.A., Irving, J.A.
Funding Organization(s): Medical Research Council (United Kingdom), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.223 (Depositor), 0.237 (DCC)
R-Value Work:
0.201 (Depositor)
R-Value Observed:
0.202 (Depositor)

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

Literature

Polymer accumulation in alpha-1 antitrypsin deficiency

Wan, M., Ronzoni, R., Irving, J.A., Lomas, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 45.74 kDa
Atom Count: 3,060
Modeled Residue Count: 367
Deposited Residue Count: 404
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1-antitrypsin	A	404	Homo sapiens	Mutation(s): 3 Gene Names: SERPINA1, AAT, PI, PRO0684, PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens) Explore P01009 Go to UniProtKB: P01009
PHAROS: P01009 GTEx: ENSG00000197249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01009
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.223 (Depositor), 0.237 (DCC)
R-Value Work: 0.201 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.462	α = 90
b = 38.958	β = 103.91
c = 90.016	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N024842/1
Other government	United Kingdom	UCLH/NIHR Biomedical Research Centre

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, 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.