7D5Y | pdb_00007d5y

Cystein protease domain from MARTX toxin

PDB DOI: https://doi.org/10.2210/pdb7D5Y/pdb

Classification: TOXIN
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-28 Released: 2021-05-12
Deposition Author(s): Kim, M.-H., Hwang, J., Choi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.217 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (Depositor)

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

Literature

Cystein protease domain from MARTX toxin

Kim, M.-H., Hwang, J., Choi, S.

To be published.

Macromolecule Content

Total Structure Weight: 23.23 kDa
Atom Count: 1,732
Modeled Residue Count: 210
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MARTX	A	210	Vibrio vulnificus	Mutation(s): 0
UniProt
Find proteins for A0A023NA98 (Vibrio vulnificus) Explore A0A023NA98 Go to UniProtKB: A0A023NA98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A023NA98
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 C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.189 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.307	α = 90
b = 125.307	β = 90
c = 125.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2023-11-29
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.