3WT1 | pdb_00003wt1

Crystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (reduced form)

PDB DOI: https://doi.org/10.2210/pdb3WT1/pdb

Classification: ISOMERASE
Organism(s): Mycothermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-04-02 Released: 2014-11-26
Deposition Author(s): Inagaki, K., Satoh, T., Itoh, S.G., Okumura, H., Kato, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.278 (Depositor), 0.287 (DCC)
R-Value Work:
0.238 (Depositor)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation

Inagaki, K., Satoh, T., Itoh, S.G., Okumura, H., Kato, K.

(2015) Chem Phys Lett 618: 203-207

DOI: https://doi.org/10.1016/j.cplett.2014.11.017

Macromolecule Content

Total Structure Weight: 108.42 kDa
Atom Count: 7,831
Modeled Residue Count: 970
Deposited Residue Count: 988
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein disulfide-isomerase	A, B, C, D	247	Mycothermus thermophilus	Mutation(s): 0 EC: 5.3.4.1
UniProt
Find proteins for P55059 (Humicola insolens) Explore P55059 Go to UniProtKB: P55059
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55059
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.278 (Depositor), 0.287 (DCC)
R-Value Work: 0.238 (Depositor)
R-Value Observed: 0.240 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.77	α = 105.92
b = 67.75	β = 113.13
c = 70.25	γ = 96.59

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2014-12-03
Changes: Database references
Version 1.2: 2014-12-31
Changes: Database references
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.