9WQU | pdb_00009wqu

b-b' domain fragment of ER-60 (ERp57) under microgravity

PDB DOI: https://doi.org/10.2210/pdb9WQU/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-11 Released: 2025-10-01
Deposition Author(s): Furubayashi, N., Shinohara, Y., Inaka, K., Kaito, S., Kobayashi, Y., Kamo, M., Urade, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.263 (Depositor), 0.257 (DCC)
R-Value Work:
0.219 (Depositor), 0.214 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of b-b' domain fragment of ER-60 (ERp57) under microgravity

Furubayashi, N., Shinohara, Y., Inaka, K., Kaito, S., Kobayashi, Y., Kamo, M., Urade, R.

To be published.

Macromolecule Content

Total Structure Weight: 85.94 kDa
Atom Count: 6,220
Modeled Residue Count: 699
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase A3	A, B, C	252	Homo sapiens	Mutation(s): 0 Gene Names: PDIA3, ERP57, ERP60, GRP58 EC: 5.3.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30101 (Homo sapiens) Explore P30101 Go to UniProtKB: P30101
PHAROS: P30101 GTEx: ENSG00000167004
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30101
Sequence Annotations Expand
Reference Sequence

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 D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.263 (Depositor), 0.257 (DCC)
R-Value Work: 0.219 (Depositor), 0.214 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.315	α = 90
b = 62.901	β = 98.64
c = 97.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Furubayashi, N.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18380079
Japan Society for the Promotion of Science (JSPS)	Japan	21380081
Japan Society for the Promotion of Science (JSPS)	Japan	25292070

Revision History (Full details and data files)

Version 1.0: 2025-10-01
Type: Initial release

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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.